Aad-1  event das-40278-9, related transgenic corn lines, and event-specific identification thereof

ABSTRACT

This invention relates in part to plant breeding and herbicide tolerant plants. This invention includes a novel AAD-1 transformation event in corn plants comprising a polynucleotide sequence, as described herein, inserted into a specific site within the genome of a corn cell. In some embodiments, said event/polynucleotide sequence can be “stacked” with other traits, including, for example, other herbicide tolerance gene(s) and/or insect-inhibitory proteins. Additionally, the subject invention provides assays for detecting the presence of the subject event in a sample (or corn grain, for example). The assays can be based on the DNA sequence of the recombinant construct, inserted into the corn genome, and on the genomic sequences flanking the insertion site. Kits and conditions useful in conducting the assays are also provided.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.16/279,055, filed on Feb. 19, 2019, which is a continuation of U.S.application Ser. No. 14/989,787, filed Jan. 6, 2016 (now U.S. Pat. No.10,323,287), which is a divisional of U.S. application Ser. No.13/390,969, filed May 7, 2012 (now U.S. Pat. No. 9,402,358), which is anational stage entry of PCT/US2010/045869, filed Aug. 18, 2010 whichclaims priority to U.S. Provisional Patent Application No. 61/235,248,filed on Aug. 19, 2009, the disclosures of which are each incorporatedby reference in their entirety into the present application.

INCORPORATION BY REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY

Incorporated by reference in its entirety is a computer-readablenucleotide/amino acid sequence listing submitted concurrently herewithas an 18 kilobyte ASCII (Text) file named “344351_ST25.txt”, created onJul. 19, 2021.

BACKGROUND OF THE INVENTION

The aad-1 gene (originally from Sphingobium herbicidovorans) encodes thearyloxyalkanoate dioxygenase (AAD-1) protein. The trait conferstolerance to 2,4-dichlorophenoxyacetic acid and aryloxyphenoxypropionate(commonly referred to as “fop” herbicides such as quizalofop) herbicidesand may be used as a selectable marker during plant transformation andin breeding nurseries. The aad-1 gene, itself, for herbicide tolerancein plants was first disclosed in WO 2005/107437 (see also US2009-0093366).

The expression of heterologous or foreign genes in plants is influencedby where the foreign gene is inserted in the chromosome. This could bedue to chromatin structure (e.g., heterochromatin) or the proximity oftranscriptional regulation elements (e.g., enhancers) close to theintegration site (Weising et al., Ann. Rev. Genet. 22:421-477, 1988),for example. The same gene in the same type of transgenic plant (orother organism) can exhibit a wide variation in expression level amongstdifferent events. There may also be differences in spatial or temporalpatterns of expression. For example, differences in the relativeexpression of a transgene in various plant tissues may not correspond tothe patterns expected from transcriptional regulatory elements presentin the introduced gene construct.

Thus, large numbers of events are often created and screened in order toidentify an event that expresses an introduced gene of interest to asatisfactory level for a given purpose. For commercial purposes, it iscommon to produce hundreds to thousands of different events and toscreen those events for a single event that has desired transgeneexpression levels and patterns. An event that has desired levels and/orpatterns of transgene expression is useful for introgressing thetransgene into other genetic backgrounds by sexual outcrossing usingconventional breeding methods. Progeny of such crosses maintain thetransgene expression characteristics of the original transformant. Thisstrategy is used to ensure reliable gene expression in a number ofvarieties that are well adapted to local growing conditions.

U.S. Patent Apps. 20020120964 A1 and 20040009504 A1 relate to cottonevent PV-GHGT07(1445) and compositions and methods for the detectionthereof. WO 02/100163 relates to cotton event MONI5985 and compositionsand methods for the detection thereof. WO 2004/011601 relates to cornevent MON863 plants and compositions and methods for the detectionthereof. WO 2004/072235 relates to cotton event MON 88913 andcompositions and methods for the detection thereof.

WO 2006/098952 relates to corn event 3272. WO 2007/142840 relates tocorn event MIR162.

U.S. Pat. No. 7,179,965 relates to cotton having a cry1F event and acry1Ac event.

AAD-1 corn having the specific event disclosed herein has not previouslybeen disclosed.

BRIEF SUMMARY OF THE INVENTION

The present invention is related to the AAD-1 corn event designatedDAS-40278-9 having seed deposited with American Type Culture Collection(ATCC) with Accession No. PTA-10244, and progeny derived thereof. Otheraspects of the invention comprise the progeny plants, seeds and grain orregenerable parts of the plants and seeds and progeny of corn eventDAS-40278-9, as well as food or feed products made from any thereof. Theinvention also includes plant parts of corn event DAS-40278-9 thatinclude, but are not limited to, pollen, ovule, flowers, shoots, roots,and leaves, and nuclei of vegetative cells, pollen cells, and egg cells.The invention further relates to corn plants having tolerance to phenoxyauxinic and/or aryloxyalkanoate herbicides, novel genetic compositionsof corn event DAS-40278-9, and aspects of agronomic performance of cornplants comprising corn event DAS-40278-9.

This invention relates in part to plant breeding and herbicide tolerantplants. This invention includes a novel aad-1 transformation event incorn plants comprising a polynucleotide sequence, as described herein,inserted into a specific site within the genome of a corn cell.

In some embodiments, said event/polynucleotide sequence can be “stacked”with other traits, including, for example, other herbicide tolerancegene(s) and/or insect-inhibitory proteins. However, the subjectinvention includes plants having the single event, as described herein.

The additional traits may be stacked into the plant genome via plantbreeding, re-transformation of the transgenic plant containing cornevent DAS-40278-9, or addition of new traits through targetedintegration via homologous recombination.

Other embodiments include the excision of polynucleotide sequences whichcomprise corn event DAS-40278-9, including for example, the pat geneexpression cassette. Upon excision of a polynucleotide sequence, themodified event may be re-targeted at a specific chromosomal site whereinadditional polynucleotide sequences are stacked with corn eventDAS-40278-9.

In one embodiment, the present invention encompasses a corn chromosomaltarget site located on chromosome 2 at approximately 20 cM between SSRmarkers UMC1265 (see SEQ ID) NO:30 and SEQ ID NO:31) and MMC0111 (seeSEQ ID NO:32 and SEQ ID NO:33) at approximately 20 cM on the 2008 DAScorn linkage map, wherein the target site comprises a heterologousnucleic acid. In another embodiment, the present invention encompasses acorn chromosomal target site comprising a location defined in or by SEQID NO:29 and the residues thereof as described herein, as would berecognized by one skilled in the art.

In one embodiment, the present invention encompasses a method of makinga transgenic corn plant comprising inserting a heterologous nucleic acidat a position on chromosome 2 at approximately 20 cM between SSR markersUMC1265 (see SEQ ID NO:30 and SEQ ID NO:31) and MMC0111 (see SEQ IDNO:32 and SEQ ID NO:33) at approximately 20 cM on the 2008 DAS cornlinkage map. In still another embodiment, the inserted heterologousnucleic acid is flanked 5′ by all or part of the 5′ flanking sequence asdefined herein with reference to SEQ ID NO:29, and flanked 3′ by all orpart of the 5′ flanking sequence as defined herein with reference to SEQID NO:29.

Additionally, the subject invention provides assays for detecting thepresence of the subject event in a sample (of corn grain, for example).The assays can be based on the DNA sequence of the recombinantconstruct, inserted into the corn genome, and on the genomic sequencesflanking the insertion site. Kits and conditions useful in conductingthe assays are also provided.

Thus, the subject invention relates in part to the cloning and analysisof the DNA sequences of a whole AAD-1 insert, and the border regionsthereof (in transgenic corn lines). These sequences are unique. Based onthese insert and border sequences, event-specific primers weregenerated. PCR analysis demonstrated that these events can be identifiedby analysis of the PCR amplicons generated with these event-specificprimer sets. Thus, these and other related procedures can be used touniquely identify corn lines comprising the event of the subjectinvention.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a plasmid map of pDAS 1740.

FIG. 2 shows components of the insert for DAS-40278-9 (pDAS 1740).

FIG. 3 shows a restriction map and components of the insert forDAS-40278-9 (pDAS 1740).

FIG. 4 shows amplicons, primers, and a cloning strategy for the DNAinsert and borders for DAS-40278-9.

FIG. 5 illustrates primer locations with respect to the insert andborders for DAS-40278-9.

FIG. 6 illustrates the junction regions and insertion for DAS-40278-9.

FIG. 7 is a breeding diagram referenced in Example 7.

BRIEF DESCRIPTION OF THE SEQUENCES

SEQ ID NOs: 1-28 are primers as described herein.

SEQ ID NO:29 provides insert and flanking sequences for the subjectevent DAS-40278-9.

SEQ ID NOs: 30-33 are primers for flanking markers as described inExample 4.

DETAILED DESCRIPTION OF THE INVENTION

This invention relates in part to plant breeding and herbicide tolerantplants. This invention includes novel transformation events of cornplants (maize) comprising a subject aad-1 polynucleotide sequences, asdescribed herein, inserted into specific site within the genome of acorn cell. In some embodiments, said polynucleotide sequence can be“stacked” with other traits (such as other herbicide tolerance gene(s)and/or gene(s) that encode insect-inhibitory proteins, for example. Insome embodiments said polynucleotide sequences can be excised andsubsequently re-targeted with additional polynucleotide sequences.However, the subject invention includes plants having a single event, asdescribed herein.

Additionally, the subject invention provides assays for detecting thepresence of the subject event in a sample. Aspects of the subjectinvention include methods of designing and/or producing any diagnosticnucleic acid molecules exemplified or suggested herein, particularlythose based wholly or partially on the subject flanking sequences.

More specifically, the subject invention relates in part to transgeniccorn event DAS-40278-9 (also known as pDAS 1740-278), plant linescomprising these events, and the cloning and analysis of the DNAsequences of this insert, and/or the border regions thereof. Plant linesof the subject invention can be detected using sequences disclosed andsuggested herein.

In some embodiments, this invention relates to herbicide-tolerant cornlines, and the identification thereof. The subject invention relates inpart to detecting the presence of the subject event in order todetermine whether progeny of a sexual cross contain the event ofinterest. In addition, a method for detecting the event is included andis helpful, for example, for complying with regulations requiring thepre-market approval and labeling of foods derived from recombinant cropplants, for example. It is possible to detect the presence of thesubject event by any well-known nucleic acid detection method such aspolymerase chain reaction (PCR) or DNA hybridization using nucleic acidprobes. An event-specific PCR assay is discussed, for example, byWindels et al. (Med. Fac. Landbouww, Univ. Gent 64/5b:459462, 1999).This related to the identification of glyphosate tolerant soybean event40-3-2 by PCR using a primer set spanning the junction between theinsert and flanking DNA. More specifically, one primer included sequencefrom the insert and a second primer included sequence from flanking DNA.

Corn was modified by the insertion of the aad-1 gene from Sphingobiumherbicidovorans which encodes the aryloxyalkanoate dioxygenase (AAD-1)protein. The trait confers tolerance to 2,4-dichlorophenoxyacetic acidand aryloxyphenoxypropionate (commonly referred to as “fop” herbicidessuch as quizalofop) herbicides and may be used as a selectable markerduring plant transformation and in breeding nurseries. Transformation ofcorn with a DNA fragment from the plasmid pDAS1740 was carried forward,through breeding, to produce event DAS-40278-9.

Genomic DNA samples extracted from twenty individual corn plants derivedfrom five generations and four plants per generation of eventDAS-40278-9 were selected for molecular characterization of the AAD-1corn event DAS-40278-9. AAD-1 protein expression was tested using anAAD-1 specific rapid test strip kit. Only plants that tested positivefor AAD-1 protein expression were selected for subsequent molecularcharacterization. Southern hybridization confirmed that the aad-1 geneis present in corn plants that tested positive for AAD-1 proteinexpression, and the aad-1 gene was inserted as a single intact copy inthese plants when hybridized with an aad-1 gene probe.

Molecular characterization of the inserted DNA in AAD-1 corn eventDAS-40278-9 is also described herein. The event was produced viaWhiskers transformation with the Fsp I fragment of plasmid pDAS 1740.Southern blot analysis was used to establish the integration pattern ofthe inserted DNA fragment and determine insert/copy number of the aad-1gene in event DAS-40278-9. Data were generated to demonstrate theintegration and integrity of the aad-1 transgene inserted into the corngenome. Characterization of the integration of noncoding regions(designed to regulate the coding regions), such as promoters andterminators, the matrix attachment regions RB7 Mar v3 and RB7 Mar v4, aswell as stability of the transgene insert across generations, wereevaluated. The stability of the inserted DNA was demonstrated acrossfive distinct generations of plants. Furthermore, absence oftransformation plasmid backbone sequence including the Ampicillinresistance gene (Apr) region was demonstrated by probes covering nearlythe whole backbone region flanking the restriction sites (Fsp I) ofplasmid pDAS 1740. A detailed physical map of the insertion was drawnbased on these Southern blot analyses of event DAS-40278-9.

Levels of AAD-1 protein were determined in corn tissues. In addition,compositional analysis was performed on corn forage and grain toinvestigate the equivalency between the isogenic non-transformed cornline and the transgenic corn line DAS-40278-9 (unsprayed, sprayed with2,4-D, sprayed with quizalofop, and sprayed with 2,4-D and quizalofop).Agronomic characteristics of the isogenic non-transformed corn line werealso compared to the DAS-40278-9 corn.

Field expression, nutrient composition, and agronomic trials of anon-transgenic control and a hybrid corn line containingAryloxyalkanoate Dioxygenase-1 (AAD-1) were conducted in the same yearat six sites located in Iowa, Illinois (2 sites), Indiana, Nebraska andOntario, Canada. Expression levels are summarized herein for the AAD-1protein in leaf, pollen, root, forage, whole plant, and grain, theresults of agronomic determinations, and compositional analysis offorage and grain samples from the control and DAS-40278-9 AAD-1 corn.

The soluble, extractable AAD-1 protein was measured using a quantitativeenzyme-linked immunosorbent assay (ELISA) method in corn leaf, pollen,root, forage, whole plant, and grain. Good average expression valueswere observed in root and pollen tissue, as discussed in more detailherein. Expression values were similar for all the sprayed treatments aswell as for the plots sprayed and unsprayed with 2,4-D and quizalofopherbicides.

Compositional analyses, including proximates, minerals, amino acids,fatty acids, vitamins, anti-nutrients, and secondary metabolites wereconducted to investigate the equivalency of DAS-40278-9 AAD-1 corn (withor without herbicide treatments) to the control. Results for DAS-40278-9AAD-1 composition samples were all as good as, or better than(biologically and agronomically), based on control lines and/orconventional corn, analysis of agronomic data collected from control andDAS-40278-9 AAD-1 corn plots.

As alluded to above in the Background section, the introduction andintegration of a transgene into a plant genome involves some randomevents (hence the name “event” for a given insertion that is expressed).That is, with many transformation techniques such as Agrobacteriumtransformation, the “gene gun,” and WHISKERS, it is unpredictable wherein the genome a transgene will become inserted. Thus, identifying theflanking plant genomic DNA on both sides of the insert can be importantfor identifying a plant that has a given insertion event. For example,PCR primers can be designed that generate a PCR amplicon across thejunction region of the insert and the host genome. This PCR amplicon canbe used to identify a unique or distinct type of insertion event.

As “events” are originally random events, as part of this disclosure atleast 2500 seeds of a corn line comprising the event have been depositedand made available to the public without restriction (but subject topatent rights), with the American Type Culture Collection (ATCC), 10801University Boulevard, Manassas, Va., 20110. The deposit has beendesignated as ATCC Deposit No. PTA-10244 (Yellow Dent maize hybrid seed(Zea Mays L.):DAS-40278-9; Deposited on behalf of Dow AgroSciences LLC;Date of receipt of seeds/strain(s) by the ATTC: Jul. 10, 2009; viabilityconfirmed Aug. 17, 2009). This deposit was made and will be maintainedin accordance with and under the terms of the Budapest Treaty withrespect to seed deposits for the purposes of patent procedure. Thedeposit will be maintained without restriction at the ATCC depository,which is a public depository, for a period of 30 years, or five yearsafter the most recent request, or for the effective life of the patent,whichever is longer, and will be replaced if it becomes nonviable duringthat period.

The deposited seeds are part of the subject invention. Clearly, cornplants can be grown from these seeds, and such plants are part of thesubject invention. The subject invention also relates to DNA sequencescontained in these corn plants that are useful for detecting theseplants and progeny thereof. Detection methods and kits of the subjectinvention can be directed to identifying any one, two, or even all threeof these events, depending on the ultimate purpose of the test.

Definitions and examples are provided herein to help describe thepresent invention and to guide those of ordinary skill in the art topractice the invention. Unless otherwise noted, terms are to beunderstood according to conventional usage by those of ordinary skill inthe relevant art. The nomenclature for DNA bases as set forth at 37 CFR§ 1.822 is used.

As used herein, the term “progeny” denotes the offspring of anygeneration of a parent plat which comprises AAD-1 corn evendDAS-40278-9.

A transgenic “event” is produced by transformation of plant cells withheterologous DNA, i.e., a nucleic acid construct that includes atransgene of interest, regeneration of a population of plants resultingfrom the insertion of the transgene into the genome of the plant, andselection of a particular plant characterized by insertion into aparticular genome location. The term “event” refers to the originaltransformant and progeny of the transformant that include theheterologous DNA. The term “event” also refers to progeny produced by asexual outcross between the transformant and another variety thatincludes the genomic/transgene DNA. Even after repeated back-crossing toa recurrent parent, the inserted transgene DNA and flanking genomic DNA(genomic/transgene DNA) from the transformed parent is present in theprogeny of the cross at the same chromosomal location. The term “event”also refers to DNA from the original transformant and progeny thereofcomprising the inserted DNA and flanking genomic sequence immediatelyadjacent to the inserted DNA that would be expected to be transferred toa progeny that receives inserted DNA including the transgene of interestas the result of a sexual cross of one parental line that includes theinserted DNA (e.g., the original transformant and progeny resulting fromselfing) and a parental line that does not contain the inserted DNA.

A “junction sequence” spans the point at which DNA inserted into thegenome is linked to DNA from the corn native genome flanking theinsertion point, the identification or detection of one or the otherjunction sequences in a plant's genetic material being sufficient to bediagnostic for the event. Included are the DNA sequences that span theinsertions in herein-described corn events and similar lengths offlanking DNA. Specific examples of such diagnostic sequences areprovided herein; however, other sequences that overlap the junctions ofthe insertions, or the junctions of the insertions and the genomicsequence, are also diagnostic and could be used according to the subjectinvention.

The subject invention relates to the identification of such flanking,junction, and insert sequences. Related PCR primers and amplicons areincluded in the invention. According to the subject invention, PCRanalysis methods using amplicons that span across inserted DNA and itsborders can be used to detect or identify commercialized transgenic cornvarieties or lines derived from the subject proprietary transgenic cornlines.

The entire sequences of each of these inserts, together with portions ofthe respective flanking sequences, are provided herein as SEQ ID NO:29.The coordinates of the insert and flanking sequences for this event withrespect to SEQ ID NO:29 (8557 basepairs total) are printed below. Thisis discussed in more detail in Example 3.8, for example.

5′ Flanking Insert 3' Flanking residue #s (SEQ: 29): 1-1873 1874-66896690-8557 length (bp): 1873 bp 4816 bp 1868 bp

This insertion event, and further components thereof, are furtherillustrated in FIGS. 1 and 2. These sequences (particularly the flankingsequences) are unique. Based on these insert and border sequences,event-specific primers were generated. PCR analysis demonstrated thatthese corn lines can be identified in different corn genotypes byanalysis of the PCR amplicons generated with these event-specific primersets. Thus, these and other related procedures can be used to uniquelyidentify these corn lines. The sequences identified herein are unique.For example, BLAST searches against GENBANK databases did not reveal anysignificant homology between the cloned border sequences and sequencesin the database.

Detection techniques of the subject invention are especially useful inconjunction with plant breeding, to determine which progeny plantscomprise a given event, after a parent plant comprising an event ofinterest is crossed with another plant line in an effort to impart oneor more additional traits of interest in the progeny. These PCR analysismethods benefit corn breeding programs as well as quality control,especially for commercialized transgenic cornseeds. PCR detection kitsfor these transgenic corn lines can also now be made and used. This canalso benefit product registration and product stewardship.

Furthermore, flanking corn/genomic sequences can be used to specificallyidentify the genomic location of each insert. This information can beused to make molecular marker systems specific to each event. These canbe used for accelerated breeding strategies and to establish linkagedata.

Still further, the flanking sequence information can be used to studyand characterize transgene integration processes, genomic integrationsite characteristics, event sorting, stability of transgenes and theirflanking sequences, and gene expression (especially related to genesilencing, transgene methylation patterns, position effects, andpotential expression-related elements such as MARS [matrix attachmentregions], and the like).

In light of all the subject disclosure, it should be clear that thesubject invention includes seeds available under ATCC Deposit No.PTA-10244. The subject invention also includes a herbicide-resistantcorn plant grown from a seed deposited with the ATCC under accessionnumber PTA-10244. The subject invention further includes parts of saidplant, such as leaves, tissue samples, seeds produced by said plant,pollen, and the like.

Still further, the subject invention includes descendant and/or progenyplants of plants grown from the deposited seed, preferably aherbicide-resistant corn plant wherein said plant has a genomecomprising a detectable wild-type genomic DNA/insert DNA junctionsequence as described herein. As used herein, the term “corn” meansmaize (Zea mays) and includes all varieties thereof that can be bredwith corn.

This invention further includes processes of making crosses using aplant of the subject invention as at least one parent. For example, thesubject invention includes an F₁ hybrid plant having as one or bothparents any of the plants exemplified herein. Also within the subjectinvention is seed produced by such F₁ hybrids of the subject invention.This invention includes a method for producing an F₁ hybrid seed bycrossing an exemplified plant with a different (e.g. in-bred parent)plant and harvesting the resultant hybrid seed. The subject inventionincludes an exemplified plant that is either a female parent or a maleparent. Characteristics of the resulting plants may be improved bycareful consideration of the parent plants.

A herbicide-tolerant corn plant can be bred by first sexually crossing afirst parental corn plant consisting of a corn plant grown from seed ofany one of the lines referred to herein, and a second parental cornplant, thereby producing a plurality of first progeny plants; and thenselecting a first progeny plant that is resistant to a herbicide (orthat possesses at least one of the events of the subject invention); andselfing the first progeny plant, thereby producing a plurality of secondprogeny plants; and then selecting from the second progeny plants aplant that is resistant to a herbicide (or that possesses at least oneof the events of the subject invention). These steps can further includethe back-crossing of the first progeny plant or the second progeny plantto the second parental corn plant or a third parental corn plant. A corncrop comprising corn seeds of the subject invention, or progeny thereof,can then be planted.

It is also to be understood that two different transgenic plants canalso be mated to produce offspring that contain two independentlysegregating added, exogenous genes. Selfing of appropriate progeny canproduce plants that are homozygous for both added, exogenous genes.Back-crossing to a parental plant and out-crossing with a non-transgenicplant are also contemplated, as is vegetative propagation. Otherbreeding methods commonly used for different traits and crops are knownin the art. Backcross breeding has been used to transfer genes for asimply inherited, highly heritable trait into a desirable homozygouscultivar or inbred line, which is the recurrent parent. The source ofthe trait to be transferred is called the donor parent. The resultingplant is expected to have the attributes of the recurrent parent (e.g.,cultivar) and the desirable trait transferred from the donor parent.After the initial cross, individuals possessing the phenotype of thedonor parent are selected and repeatedly crossed (backcrossed) to therecurrent parent. The resulting parent is expected to have theattributes of the recurrent parent (e.g., cultivar) and the desirabletrait transferred from the donor parent.

The DNA molecules of the present invention can be used as molecularmarkers in a marker assisted breeding (MAB) method. DNA molecules of thepresent invention can be used in methods (such as, AFLP markers, RFLPmarkers, RAPD markers, SNPs, and SSRs) that identify genetically linkedagronomically useful traits, as is known in the art. Theherbicide-resistance trait can be tracked in the progeny of a cross witha corn plant of the subject invention (or progeny thereof and any othercorn cultivar or variety) using the MAB methods. The DNA molecules aremarkers for this trait, and MAB methods that are well known in the artcan be used to track the hebicide-resistance trait(s) in corn plantswhere at least one corn line of the subject invention, or progenythereof, was a parent or ancestor. The methods of the present inventioncan be used to identify any corn variety having the subject event.

Methods of the subject invention include a method of producing aherbicide-tolerant corn plant wherein said method comprises breedingwith a plant of the subject invention. More specifically, said methodscan comprise crossing two plants of the subject invention, or one plantof the subject invention and any other plant. Preferred methods furthercomprise selecting progeny of said cross by analyzing said progeny foran event detectable according to the subject invention. For example, thesubject invention can be used to track the subject event throughbreeding cycles with plants comprising other desirable traits, such asagronomic traits such as those tested herein in various Examples. Plantscomprising the subject event and the desired trait can be detected,identified, selected, and quickly used in further rounds of breeding,for example. The subject event/trait can also be combined throughbreeding, and tracked according to the subject invention, with an insectresistant trait(s) and/or with further herbicide tolerance traits. Onepreferred embodiment of the latter is a plant comprising the subjectevent combined with a gene encoding resistance to the herbicide dicamba.

Thus, the subject invention can be combined with, for example, traitsencoding glyphosate resistance (e.g., resistant plant or bacterialEPSPS, GOX, GAT), glufosinate resistance (e.g., Pat, bar), acetolactatesynthase (ALS)-inhibiting herbicide resistance (e.g., imidazolinones[such as imazethapyr], sulfonylureas, triazolopyrimidine sulfonanilide,pyrmidinylthiobenzoates, and other chemistries [Csr1, SurA, et al.]),bromoxynil resistance (e.g., Bxn), resistance to inhibitors of HPPD(4-hydroxlphenyl-pyruvate-dioxygenase) enzyme, resistance to inhibitorsof phytoene desaturase (PDS), resistance to photosystem II inhibitingherbicides (e.g., psbA), resistance to photosystem I inhibitingherbicides, resistance to protoporphyrinogen oxidase IX (PPO)-inhibitingherbicides (e.g., PPO-1), resistance to phenylurea herbicides (e.g.,CYP76B1), dicamba-degrading enzymes (see, e.g., US 20030135879), andothers could be stacked alone or in multiple combinations to provide theability to effectively control or prevent weed shifts and/or resistanceto any herbicide of the aforementioned classes.

Regarding additional herbicides, some additional preferred ALS (alsoknown as AHAS) inhibitors include the triazolopyrimidine sulfonanilides(such as cloransulam-methyl, diclosulam, florasulam, flumetsulam,metosulam, and penoxsulam), pyrimidinylthiobenzoates (such as bispyribacand pyrithiobac), and flucarbazone. Some preferred HPPD inhibitorsinclude mesotrione, isoxaflutole, and sulcotrione. Some preferred PPOinhibitors include flumiclorac, flumioxazin, flufenpyr, pyraflufen,fluthiacet, butafenacil, carfentrazone, sulfentrazone, and thediphenylethers (such as acifluorfen, fomesafen, lactofen, andoxyfluorfen).

Additionally, AAD-1 alone or stacked with one or more additional HTCtraits can be stacked with one or more additional input (e.g., insectresistance, fungal resistance, or stress tolerance, et al.) or output(e.g., increased yield, improved oil profile, improved fiber quality, etal.) traits. Thus, the subject invention can be used to provide acomplete agronomic package of improved crop quality with the ability toflexibly and cost effectively control any number of agronomic pests.

Methods to integrate a polynucleotide sequence within a specificchromosomal site of a plant cell via homologous recombination have beendescribed within the art. For instance, site specific integration asdescribed in US Patent Application Publication No. 2009/0111188 A1describes the use of recombinases or integrases to mediate theintroduction of a donor polynucleotide sequence into a chromosomaltarget. In addition, International Patent Application No. WO 2008/021207describes zinc finger mediated-homologous recombination to integrate oneor more donor polynucleotide sequences within specific locations of thegenome. The use of recombinases such as FLP/FRT as described in U.S.Pat. No. 6,720,475 or CRE/LOX as described in U.S. Pat. No. 5,658,772can be utilized to integrate a polynucleotide sequence into a specificchromosomal site. Finally the use of meganucleases for targeting donorpolynucleotides into a specific chromosomal location was described inPuchta et al., PNAS USA 93 (1996) pp. 5055-5060.

Other various methods for site specific integration within plant cellsare generally known and applicable (Kumar et al., Trands in Plant Sci. 6(4) (2001) pp. 155-159). Furthermore, site-specific recombinationsystems which have been identified in several prokaryotic and lowereukaryotic organisms may be applied to use in plants. Examples of suchsystems include, but are not limited too: the R/RS recombinase systemfrom the pSR1 plasmid of the yeast Zygosaccharomyces rouxii (Araki etal. (1985) J. Mol. Biol. 182: 191-203), and the Gin/gix system of phageMu (Maeser and Kahlmann (1991) Mol. Gen. Genet. 230: 170-176).

In some embodiments of the present invention, it can be desirable tointegrate or stack a new transgene(s) in proximity to an existingtransgenic event. The transgenic event can be considered a preferredgenomic locus which was selected based on unique characteristics such assingle insertion site, normal Mendelian segregation and stableexpression, and a superior combination of efficacy, including herbicidetolerance and agronomic performance in and across multiple environmentallocations. The newly integrated transgenes should maintain the transgeneexpression characteristics of the existing transformants. Moreover, thedevelopment of assays for the detection and confirmation of the newlyintegrated event would be overcome as the genomic flanking sequences andchromosomal location of the newly integrated event are alreadyidentified. Finally, the integration of a new transgene into a specificchromosomal location which is linked to an existing transgene wouldexpedite the introgression of the transgenes into other geneticbackgrounds by sexual out-crossing using conventional breeding methods.

In some embodiments of the present invention, it can be desirable toexcise polynucleotide sequences from a transgenic event. For instancetransgene excision as described in Provisional U.S. Patent ApplicationNo. 61/297,628 describes the use of zinc finger nucleases to remove apolynucleotide sequence, consisting of a gene expression cassette, froma chromosomally integrated transgenic event. The polynucleotide sequencewhich is removed can be a selectable marker. Upon excision and removalof a polynucleotide sequence the modified transgenic event can beretargeted by the insertion of a polynucleotide sequence. The excisionof a polynucleotide sequence and subsequent retargeting of the modifiedtransgenic event provides advantages such as re-use of a selectablemarker or the ability to overcome unintended changes to the planttranscriptome which results from the expression of specific genes.

The subject invention discloses herein a specific site on chromosome 2in the corn genome that is excellent for insertion of heterologousnucleic acids. Also disclosed is a 5′ molecular marker, a 3′ molecularmarker, a 5′ flanking sequence, and a 3′ flanking sequence useful inidentifying the location of a targeting site on chromosome 2. Thus, thesubject invention provides methods to introduce heterologous nucleicacids of interest into this pre-established target site or in thevicinity of this target site. The subject invention also encompasses acorn seed and/or a corn plant comprising any heterologous nucleotidesequence inserted at the disclosed target site or in the generalvicinity of such site. One option to accomplish such targetedintegration is to excise and/or substitute a different insert in placeof the pat expression cassette exemplified herein. In this generalregard, targeted homologous recombination, for example and withoutlimitation, can be used according to the subject invention.

As used herein gene, event or trait “stacking” is combining desiredtraits into one transgenic line. Plant breeders stack transgenic traitsby making crosses between parents that each have a desired trait andthen identifying offspring that have both of these desired traits.Another way to stack genes is by transferring two or more genes into thecell nucleus of a plant at the same time during transformation. Anotherway to stack genes is by re-transforming a transgenic plant with anothergene of interest. For example, gene stacking can be used to combine twoor more different traits, including for example, two or more differentinsect traits, insect resistance trait(s) and disease resistancetrait(s), two or more herbicide resistance traits, and/or insectresistance trait(s) and herbicide resistant trait(s). The use of aselectable marker in addition to a gene of interest can also beconsidered gene stacking.

“Homologous recombination” refers to a reaction between any pair ofnucleotide sequences having corresponding sites containing a similarnucleotide sequence through which the two nucleotide sequences caninteract (recombine) to form a new, recombinant DNA sequence. The sitesof similar nucleotide sequence are each referred to herein as a“homology sequence.” Generally, the frequency of homologousrecombination increases as the length of the homology sequenceincreases. Thus, while homologous recombination can occur between twonucleotide sequences that are less than identical, the recombinationfrequency (or efficiency) declines as the divergence between the twosequences increases. Recombination may be accomplished using onehomology sequence on each of the donor and target molecules, therebygenerating a “single-crossover” recombination product. Alternatively,two homology sequences may be placed on each of the target and donornucleotide sequences. Recombination between two homology sequences onthe donor with two homology sequences on the target generates a“double-crossover” recombination product. If the homology sequences onthe donor molecule flank a sequence that is to be manipulated (e.g., asequence of interest), the double-crossover recombination with thetarget molecule will result in a recombination product wherein thesequence of interest replaces a DNA sequence that was originally betweenthe homology sequences on the target molecule. The exchange of DNAsequence between the target and donor through a double-crossoverrecombination event is termed “sequence replacement.”

The subject AAD-1 enzyme enables transgenic expression resulting intolerance to combinations of herbicides that would control nearly allbroadleaf and grass weeds. AAD-1 can serve as an excellent herbicidetolerant crop (HTC) trait to stack with other HTC traits (e.g.,glyphosate resistance, glufosinate resistance, imidazolinone resistance,bromoxynil resistance, et al.), and insect resistance traits (Cry1F,Cry1Ab, Cry 34/45, et al.) for example. Additionally, AAD-1 can serve asa selectable marker to aid in selection of primary transformants ofplants genetically engineered with a second gene or group of genes.

HTC traits of the subject invention can be used in novel combinationswith other HTC traits (including but not limited to glyphosatetolerance). These combinations of traits give rise to novel methods ofcontrolling weed (and like) species, due to the newly acquiredresistance or inherent tolerance to herbicides (e.g., glyphosate). Thus,in addition to the HTC traits, novel methods for controlling weeds usingherbicides, for which herbicide tolerance was created by said enzyme intransgenic crops, are within the scope of the invention.

Additionally, glyphosate tolerant crops grown worldwide are prevalent.Many times in rotation with other glyphosate tolerant crops, control ofglyphosate-resistant volunteers may be difficult in rotational crops.Thus, the use of the subject transgenic traits, stacked or transformedindividually into crops, provides a tool for controlling other HTCvolunteer crops.

A preferred plant, or a seed, of the subject invention comprises in itsgenome the insert sequences, as identified herein, together with atleast 20-500 or more contiguous flanking nucleotides on both sides ofthe insert, as identified herein. Unless indicated otherwise, referenceto flanking sequences refers to those identified with respect to SEQ IDNO:29 (see the Table above). Again, SEQ ID NO:29 includes theheterologous DNA inserted in the original transformant and illustrativeflanking genomic sequences immediately adjacent to the inserted DNA. Allor part of these flanking sequences could be expected to be transferredto progeny that receives the inserted DNA as a result of a sexual crossof a parental line that includes the event.

The subject invention includes tissue cultures of regenerable cells of aplant of the subject invention. Also included is a plant regeneratedfrom such tissue culture, particularly where said plant is capable ofexpressing all the morphological and physiological properties of anexemplified variety. Preferred plants of the subject invention have allthe physiological and morphological characteristics of a plant grownfrom the deposited seed. This invention further comprises progeny ofsuch seed and seed possessing the quality traits of interest.

Manipulations (such as mutation, further transfection, and furtherbreeding) of plants or seeds, or parts thereof, may lead to the creationof what may be termed “essentially derived” varieties. The InternationalUnion for the Protection of New Varieties of Plants (UPOV) has providedthe following guideline for determining if a variety has beenessentially derived from a protected variety:

[A] variety shall be deemed to be essentially derived from anothervariety (“the initial variety”) when

(i) it is predominantly derived from the initial variety, or from avariety that is itself predominantly derived from the initial variety,while retaining the expression of the essential characteristics thatresult from the genotype or combination of genotypes of the initialvariety;

(ii) it is clearly distinguishable from the initial variety; and

(iii) except for the differences which result from the act ofderivation, it conforms to the initial variety in the expression of theessential characteristics that result from the genotype or combinationof genotypes of the initial variety.

UPOV, Sixth Meeting with International Organizations, Geneva, Oct. 30,1992; document prepared by the Office of the Union.

As used herein, a “line” is a group of plants that display little or nogenetic variation between individuals for at least one trait. Such linesmay be created by several generations of self-pollination and selection,or vegetative propagation from a single parent using tissue or cellculture techniques.

As used herein, the terms “cultivar” and “variety” are synonymous andrefer to a line which is used for commercial production.

“Stability” or “stable” means that with respect to the given component,the component is maintained from generation to generation and,preferably, at least three generations at substantially the same level,e.g., preferably .+−.15%, more preferably .+−.10%, most preferably.+−.5%. The stability may be affected by temperature, location, stressand the time of planting. Comparison of subsequent generations underfield conditions should produce the component in a similar manner.

“Commercial Utility” is defined as having good plant vigor and highfertility, such that the crop can be produced by farmers usingconventional farming equipment, and the oil with the describedcomponents can be extracted from the seed using conventional crushingand extraction equipment. To be commercially useful, the yield, asmeasured by seed weight, oil content, and total oil produced per acre,is within 15% of the average yield of an otherwise comparable commercialcanola variety without the premium value traits grown in the sameregion.

“Agronomically elite” means that a line has desirable agronomiccharacteristics such as yield, maturity, disease resistance, and thelike, in addition to the insect resistance due to the subject event(s).Agronomic traits, taken individually or in any combination, as set forthin Examples, below, in a plant comprising an event of the subjectinvention, are within the scope of the subject invention. Any and all ofthese agronomic characteristics and data points can be used to identifysuch plants, either as a point or at either end or both ends of a rangeof characteristics used to define such plants.

As one skilled in the art will recognize in light of this disclosure,preferred embodiments of detection kits, for example, can include probesand/or primers directed to and/or comprising “junction sequences” or“transition sequences” (where the corn genomic flanking sequence meetsthe insert sequence). For example, this includes a polynucleotideprobes, primers, and/or amplicons designed to identify one or bothjunction sequences (where the insert meets the flanking sequence), asindicated in Table 1. One common design is to have one primer thathybridizes in the flanking region, and one primer that hybridizes in theinsert. Such primers are often each about at least ˜15 residues inlength. With this arrangement, the primers can be used togenerate/amplify a detectable amplicon that indicates the presence of anevent of the subject invention. These primers can be used to generate anamplicon that spans (and includes) a junction sequence as indicatedabove.

The primer(s) “touching down” in the flanking sequence is typically notdesigned to hybridize beyond about 200 bases or beyond the junction.Thus, typical flanking primers would be designed to comprise at least 15residues of either strand within 200 bases into the flanking sequencesfrom the beginning of the insert. That is, primers comprising sequenceof an appropriate size in residues ˜1674-1873 and/or ˜6690-6890 of SEQID NO:29 are within the scope of the subject invention. Insert primerscan likewise be designed anywhere on the insert, but residues ˜1874-2074and ˜6489-6689, can be used, for example, non-exclusively for suchprimer design.

One skilled in the art will also recognize that primers and probes canbe designed to hybridize, under a range of standard hybridization and/orPCR conditions, to a segment of SEQ ID NO:29 (or the complement), andcomplements thereof, wherein the primer or probe is not perfectlycomplementary to the exemplified sequence. That is, some degree ofmismatch can be tolerated. For an approximately 20 nucleotide primer,for example, typically one or two or so nucleotides do not need to bindwith the opposite strand if the mismatched base is internal or on theend of the primer that is opposite the amplicon. Various appropriatehybridization conditions are provided below. Synthetic nucleotideanalogs, such as inosine, can also be used in probes. Peptide nucleicacid (PNA) probes, as well as DNA and RNA probes, can also be used. Whatis important is that such probes and primers are diagnostic for (able touniquely identify and distinguish) the presence of an event of thesubject invention.

It should be noted that errors in PCR amplification can occur whichmight result in minor sequencing errors, for example. That is, unlessotherwise indicated, the sequences listed herein were determined bygenerating long amplicons from corn genomic DNAs, and then cloning andsequencing the amplicons. It is not unusual to find slight differencesand minor discrepancies in sequences generated and determined in thismanner, given the many rounds of amplification that are necessary togenerate enough amplicon for sequencing from genomic DNAs. One skilledin the art should recognize and be put on notice than any adjustmentsneeded due to these types of common sequencing errors or discrepanciesare within the scope of the subject invention.

It should also be noted that it is not uncommon for some genomicsequence to be deleted, for example, when a sequence is inserted duringthe creation of an event. Thus, some differences can also appear betweenthe subject flanking sequences and genomic sequences listed in GENBANK,for example.

Some of these difference(s) are discussed below in the Examples section.Adjustments to probes and primers can be made accordingly.

The components of each of the “inserts” are illustrated in FIGS. 1 and 2and are discussed in more detail below in the Examples. The DNApolynucleotide sequences of these components, or fragments thereof, canbe used as DNA primers or probes in the methods of the presentinvention.

In some embodiments of the invention, compositions and methods areprovided for detecting the presence of the transgene/genomic insertionregion, in plants and seeds and the like, from a corn plant. DNAsequences are provided that comprise the subject transgene/genomicinsertion region junction sequence provided herein (between residues1873-1874 and 6689-6690 of SEQ ID NO:29), segments thereof, andcomplements of the exemplified sequences and any segments thereof. Theinsertion region junction sequence spans the junction betweenheterologous DNA inserted into the genome and the DNA from the corn cellflanking the insertion site. Such sequences can be diagnostic for thegiven event.

Based on these insert and border sequences, event-specific primers canbe generated. PCR analysis demonstrated that corn lines of the subjectinvention can be identified in different corn genotypes by analysis ofthe PCR amplicons generated with these event-specific primer sets. Theseand other related procedures can be used to uniquely identify these cornlines. Thus, PCR amplicons derived from such primer pairs are unique andcan be used to identify these corn lines.

In some embodiments, DNA sequences that comprise a contiguous fragmentof the novel transgene/genomic insertion region are an aspect of thisinvention. Included are DNA sequences that comprise a sufficient lengthof polynucleotides of transgene insert sequence and a sufficient lengthof polynucleotides of corn genomic sequence from one or more of thethree aforementioned corn plants and/or sequences that are useful asprimer sequences for the production of an amplicon product diagnosticfor one or more of these corn plants.

Related embodiments pertain to DNA sequences that comprise at least 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, or more contiguous nucleotides of a transgene portion of aDNA sequence identified herein (such as SEQ ID NO:29 and segmentsthereof), or complements thereof, and a similar length of flanking cornDNA sequence from these sequences, or complements thereof. Suchsequences are useful as DNA primers in DNA amplification methods. Theamplicons produced using these primers are diagnostic for any of thecorn events referred to herein. Therefore, the invention also includesthe amplicons produced by such DNA primers and homologous primers.

This invention also includes methods of detecting the presence of DNA,in a sample, that corresponds to the corn event referred to herein. Suchmethods can comprise: (a) contacting the sample comprising DNA with aprimer set that, when used in a nucleic acid amplification reaction withDNA from at least one of these corn events, produces an amplicon that isdiagnostic for said event(s); (b) performing a nucleic acidamplification reaction, thereby producing the amplicon; and (c)detecting the amplicon.

Further detection methods of the subject invention include a method ofdetecting the presence of a DNA, in a sample, corresponding to at leastone of said events, wherein said method comprises: (a) contacting thesample comprising DNA with a probe that hybridizes under stringenthybridization conditions with DNA from at least one of said corn eventsand which does not hybridize under the stringent hybridizationconditions with a control corn plant (non-event-of-interest DNA); (b)subjecting the sample and probe to stringent hybridization conditions;and (c) detecting hybridization of the probe to the DNA.

In still further embodiments, the subject invention includes methods ofproducing a corn plant comprising the aad-1 event of the subjectinvention, wherein said method comprises the steps of: (a) sexuallycrossing a first parental corn line (comprising an expression cassettesof the present invention, which confers said herbicide resistance traitto plants of said line) and a second parental corn line (that lacks thisherbicide tolerance trait) thereby producing a plurality of progenyplants; and (b) selecting a progeny plant by the use of molecularmarkers. Such methods may optionally comprise the further step ofback-crossing the progeny plant to the second parental corn line toproducing a true-breeding corn plant that comprises said insecttolerance trait.

According to another aspect of the invention, methods of determining thezygosity of progeny of a cross with any one (or more) of said threeevents are provided. Said methods can comprise contacting a sample,comprising corn DNA, with a primer set of the subject invention. Saidprimers, when used in a nucleic-acid amplification reaction with genomicDNA from at least one of said corn events, produces a first ampliconthat is diagnostic for at least one of said corn events. Such methodsfurther comprise performing a nucleic acid amplification reaction,thereby producing the first amplicon; detecting the first amplicon; andcontacting the sample comprising corn DNA with said primer set (saidprimer set, when used in a nucleic-acid amplification reaction withgenomic DNA from corn plants, produces a second amplicon comprising thenative corn genomic DNA homologous to the corn genomic region; andperforming a nucleic acid amplification reaction, thereby producing thesecond amplicon. The methods further comprise detecting the secondamplicon, and comparing the first and second amplicons in a sample,wherein the presence of both amplicons indicates that the sample isheterozygous for the transgene insertion.

DNA detection kits can be developed using the compositions disclosedherein and methods well known in the art of DNA detection. The kits areuseful for identification of the subject corn event DNA in a sample andcan be applied to methods for breeding corn plants containing this DNA.The kits contain DNA sequences homologous or complementary to theamplicons, for example, disclosed herein, or to DNA sequences homologousor complementary to DNA contained in the transgene genetic elements ofthe subject events. These DNA sequences can be used in DNA amplificationreactions or as probes in a DNA hybridization method. The kits may alsocontain the reagents and materials necessary for the performance of thedetection method.

A “probe” is an isolated nucleic acid molecule to which is attached aconventional detectable label or reporter molecule (such as aradioactive isotope, ligand, chemiluminescent agent, or enzyme). Such aprobe is complementary to a strand of a target nucleic acid, in the caseof the present invention, to a strand of genomic DNA from one of saidcorn events, whether from a corn plant or from a sample that includesDNA from the event. Probes according to the present invention includenot only deoxyribonucleic or ribonucleic acids but also polyamides andother probe materials that bind specifically to a target DNA sequenceand can be used to detect the presence of that target DNA sequence.

“Primers” are isolated/synthesized nucleic acids that are annealed to acomplementary target DNA strand by nucleic acid hybridization to form ahybrid between the primer and the target DNA strand, then extended alongthe target DNA strand by a polymerase, e.g., a DNA polymerase. Primerpairs of the present invention refer to their use for amplification of atarget nucleic acid sequence, e.g., by the polymerase chain reaction(PCR) or other conventional nucleic-acid amplification methods.

Probes and primers are generally 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87,88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146,147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160,161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174,175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188,189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202,203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216,217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230,231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244,245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258,259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272,273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300,301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314,315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328,329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342,343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356,357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370,371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384,385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398,399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412,413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426,427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440,441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454,455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468,469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482,483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496,497, 498, 499, or 500 polynucleotides or more in length. Such probes andprimers hybridize specifically to a target sequence under highstringency hybridization conditions. Preferably, probes and primersaccording to the present invention have complete sequence similaritywith the target sequence, although probes differing from the targetsequence and that retain the ability to hybridize to target sequencesmay be designed by conventional methods.

Methods for preparing and using probes and primers are described, forexample, in Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3,ed. Sambrook et al., Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y., 1989. PCR-primer pairs can be derived from a knownsequence, for example, by using computer programs intended for thatpurpose.

Primers and probes based on the flanking DNA and insert sequencesdisclosed herein can be used to confirm (and, if necessary, to correct)the disclosed sequences by conventional methods, e.g., by re-cloning andsequencing such sequences.

The nucleic acid probes and primers of the present invention hybridizeunder stringent conditions to a target DNA sequence. Any conventionalnucleic acid hybridization or amplification method can be used toidentify the presence of DNA from a transgenic event in a sample.Nucleic acid molecules or fragments thereof are capable of specificallyhybridizing to other nucleic acid molecules under certain circumstances.As used herein, two nucleic acid molecules are said to be capable ofspecifically hybridizing to one another if the two molecules are capableof forming an anti-parallel, double-stranded nucleic acid structure. Anucleic acid molecule is said to be the “complement” of another nucleicacid molecule if they exhibit complete complementarity. As used herein,molecules are said to exhibit “complete complementarity” when everynucleotide of one of the molecules is complementary to a nucleotide ofthe other. Two molecules are said to be “minimally complementary” ifthey can hybridize to one another with sufficient stability to permitthem to remain annealed to one another under at least conventional“low-stringency” conditions. Similarly, the molecules are said to be“complementary” if they can hybridize to one another with sufficientstability to permit them to remain annealed to one another underconventional “high-stringency” conditions. Conventional stringencyconditions are described by Sambrook et al., 1989. Departures fromcomplete complementarity are therefore permissible, as long as suchdepartures do not completely preclude the capacity of the molecules toform a double-stranded structure. In order for a nucleic acid moleculeto serve as a primer or probe it need only be sufficiently complementaryin sequence to be able to form a stable double-stranded structure underthe particular solvent and salt concentrations employed.

As used herein, a substantially homologous sequence is a nucleic acidsequence that will specifically hybridize to the complement of thenucleic acid sequence to which it is being compared under highstringency conditions. The term “stringent conditions” is functionallydefined with regard to the hybridization of a nucleic-acid probe to atarget nucleic acid (i.e., to a particular nucleic-acid sequence ofinterest) by the specific hybridization procedure discussed in Sambrooket al., 1989, at 9.52-9.55. See also, Sambrook et al., 1989 at 9.47-9.52and 9.56-9.58. Accordingly, the nucleotide sequences of the inventionmay be used for their ability to selectively form duplex molecules withcomplementary stretches of DNA fragments.

Depending on the application envisioned, one can use varying conditionsof hybridization to achieve varying degrees of selectivity of probetowards target sequence. For applications requiring high selectivity,one will typically employ relatively stringent conditions to form thehybrids, e.g., one will select relatively low salt and/or hightemperature conditions, such as provided by about 0.02 M to about 0.15 MNaCl at temperatures of about 50° C. to about 70° C. Stringentconditions, for example, could involve washing the hybridization filterat least twice with high-stringency wash buffer (0.2×SSC, 0.1% SDS, 65°C.). Appropriate stringency conditions which promote DNA hybridization,for example, 6.0× sodium chloride/sodium citrate (SSC) at about 45° C.,followed by a wash of 2.0×SSC at 50° C. are known to those skilled inthe art, 6.3.1-6.3.6. For example, the salt concentration in the washstep can be selected from a low stringency of about 2.0×SSC at 50° C. toa high stringency of about 0.2×SSC at 50° C. In addition, thetemperature in the wash step can be increased from low stringencyconditions at room temperature, about 22° C., to high stringencyconditions at about 65° C. Both temperature and salt may be varied, oreither the temperature or the salt concentration may be held constantwhile the other variable is changed. Such selective conditions toleratelittle, if any, mismatch between the probe and the template or targetstrand. Detection of DNA sequences via hybridization is well-known tothose of skill in the art, and the teachings of U.S. Pat. Nos. 4,965,188and 5,176,995 are exemplary of the methods of hybridization analyses.

In a particularly preferred embodiment, a nucleic acid of the presentinvention will specifically hybridize to one or more of the primers (oramplicons or other sequences) exemplified or suggested herein, includingcomplements and fragments thereof, under high stringency conditions. Inone aspect of the present invention, a marker nucleic acid molecule ofthe present invention has the nucleic acid sequence set forth in SEQ IDNOS:3-14, or complements and/or fragments thereof.

In another aspect of the present invention, a marker nucleic acidmolecule of the present invention shares between 80% and 100% or 90% and100% sequence identity with such nucleic acid sequences. In a furtheraspect of the present invention, a marker nucleic acid molecule of thepresent invention shares between 95% and 100% sequence identity withsuch sequence. Such sequences may be used as markers in plant breedingmethods to identify the progeny of genetic crosses. The hybridization ofthe probe to the target DNA molecule can be detected by any number ofmethods known to those skilled in the art, these can include, but arenot limited to, fluorescent tags, radioactive tags, antibody based tags,and chemiluminescent tags.

Regarding the amplification of a target nucleic acid sequence (e.g., byPCR) using a particular amplification primer pair, “stringentconditions” are conditions that permit the primer pair to hybridize onlyto the target nucleic-acid sequence to which a primer having thecorresponding wild-type sequence (or its complement) would bind andpreferably to produce a unique amplification product, the amplicon.

The term “specific for (a target sequence)” indicates that a probe orprimer hybridizes under stringent hybridization conditions only to thetarget sequence in a sample comprising the target sequence.

As used herein, “amplified DNA” or “amplicon” refers to the product ofnucleic-acid amplification of a target nucleic acid sequence that ispart of a nucleic acid template. For example, to determine whether thecorn plant resulting from a sexual cross contains transgenic eventgenomic DNA from the corn plant of the present invention, DNA extractedfrom a corn plant tissue sample may be subjected to nucleic acidamplification method using a primer pair that includes a primer derivedfrom flanking sequence in the genome of the plant adjacent to theinsertion site of inserted heterologous DNA, and a second primer derivedfrom the inserted heterologous DNA to produce an amplicon that isdiagnostic for the presence of the event DNA. The amplicon is of alength and has a sequence that is also diagnostic for the event. Theamplicon may range in length from the combined length of the primerpairs plus one nucleotide base pair, and/or the combined length of theprimer pairs plus about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87,88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146,147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160,161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174,175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188,189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202,203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216,217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230,231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244,245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258,259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272,273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300,301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314,315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328,329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342,343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356,357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370,371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384,385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398,399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412,413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426,427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440,441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454,455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468,469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482,483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496,497, 498, 499, or 500, 750, 1000, 1250, 1500, 1750, 2000, or morenucleotide base pairs (plus or minus any of the increments listedabove). Alternatively, a primer pair can be derived from flankingsequence on both sides of the inserted DNA so as to produce an ampliconthat includes the entire insert nucleotide sequence. A member of aprimer pair derived from the plant genomic sequence may be located adistance from the inserted DNA sequence. This distance can range fromone nucleotide base pair up to about twenty thousand nucleotide basepairs. The use of the term “amplicon” specifically excludes primerdimers that may be formed in the DNA thermal amplification reaction.

Nucleic-acid amplification can be accomplished by any of the variousnucleic-acid amplification methods known in the art, including thepolymerase chain reaction (PCR). A variety of amplification methods areknown in the art and are described, inter alia, in U.S. Pat. Nos.4,683,195 and 4,683,202. PCR amplification methods have been developedto amplify up to 22 kb of genomic DNA. These methods as well as othermethods known in the art of DNA amplification may be used in thepractice of the present invention. The sequence of the heterologoustransgene DNA insert or flanking genomic sequence from a subject cornevent can be verified (and corrected if necessary) by amplifying suchsequences from the event using primers derived from the sequencesprovided herein followed by standard DNA sequencing of the PCR ampliconor of the cloned DNA.

The amplicon produced by these methods may be detected by a plurality oftechniques. Agarose gel electrophoresis and staining with ethidiumbromide is a common well known method of detecting DNA amplicons.Another such method is Genetic Bit Analysis where an DNA oligonucleotideis designed which overlaps both the adjacent flanking genomic DNAsequence and the inserted DNA sequence. The oligonucleotide isimmobilized in wells of a microwell plate. Following PCR of the regionof interest (using one primer in the inserted sequence and one in theadjacent flanking genomic sequence), a single-stranded PCR product canbe hybridized to the immobilized oligonucleotide and serve as a templatefor a single base extension reaction using a DNA polymerase and labelledddNTPs specific for the expected next base. Readout may be fluorescentor ELISA-based. A signal indicates presence of the insert/flankingsequence due to successful amplification, hybridization, and single baseextension.

Another method is the Pyrosequencing technique as described by Winge(Innov. Pharma. Tech. 00:18-24, 2000). In this method an oligonucleotideis designed that overlaps the adjacent genomic DNA and insert DNAjunction. The oligonucleotide is hybridized to single-stranded PCRproduct from the region of interest (one primer in the inserted sequenceand one in the flanking genomic sequence) and incubated in the presenceof a DNA polymerase, ATP, sulfurylase, luciferase, apyrase, adenosine 5′phosphosulfate and luciferin. DNTPs are added individually and theincorporation results in a light signal that is measured. A light signalindicates the presence of the transgene insert/flanking sequence due tosuccessful amplification, hybridization, and single or multi-baseextension.

Fluorescence Polarization is another method that can be used to detectan amplicon of the present invention. Following this method, anoligonucleotide is designed which overlaps the genomic flanking andinserted DNA junction. The oligonucleotide is hybridized tosingle-stranded PCR product from the region of interest (one primer inthe inserted DNA and one in the flanking genomic DNA sequence) andincubated in the presence of a DNA polymerase and a fluorescent-labeledddNTP. Single base extension results in incorporation of the ddNTP.Incorporation can be measured as a change in polarization using afluorometer. A change in polarization indicates the presence of thetransgene insert/flanking sequence due to successful amplification,hybridization, and single base extension.

TAQMAN (PE Applied Biosystems, Foster City, Calif.) is a method ofdetecting and quantifying the presence of a DNA sequence. Briefly, aFRET oligonucleotide probe is designed that overlaps the genomicflanking and insert DNA junction. The FRET probe and PCR primers (oneprimer in the insert DNA sequence and one in the flanking genomicsequence) are cycled in the presence of a thermostable polymerase anddNTPs. During specific amplification, Taq DNA polymerase cleans andreleases the fluorescent moiety away from the quenching moiety on theFRET probe. A fluorescent signal indicates the presence of theflanking/transgene insert sequence due to successful amplification andhybridization.

Molecular Beacons have been described for use in sequence detection.Briefly, a FRET oligonucleotide probe is designed that overlaps theflanking genomic and insert DNA junction. The unique structure of theFRET probe results in it containing secondary structure that keeps thefluorescent and quenching moieties in close proximity. The FRET probeand PCR primers (one primer in the insert DNA sequence and one in theflanking genomic sequence) are cycled in the presence of a thermostablepolymerase and dNTPs. Following successful PCR amplification,hybridization of the FRET probe to the target sequence results in theremoval of the probe secondary structure and spatial separation of thefluorescent and quenching moieties. A fluorescent signal results. Afluorescent signal indicates the presence of the flankinggenomic/transgene insert sequence due to successful amplification andhybridization.

Having disclosed a location in the corn genome that is excellent for aninsertion, the subject invention also comprises a corn seed and/or acorn plant comprising at least one non-aad 1 insert in the generalvicinity of this genomic location. One option is to substitute adifferent insert in place of the aad-1 insert exemplified herein. Inthese generally regards, targeted homologous recombination, for example,can be used according to the subject invention. This type of technologyis the subject of for example, WO 03/080809 A2 and the correspondingpublished U.S. application (US 20030232410). Thus, the subject inventionincludes plants and plant cells comprising a heterologous insert (inplace of or with multi-copies of aad-1), flanked by all or arecognizable part of the flanking sequences identified herein (e.g.residues 1-1873 and 6690-8557 of SEQ ID NO:29).

All patents, patent applications, provisional applications, andpublications referred to or cited herein are incorporated by referencein their entirety to the extent they are not inconsistent with theexplicit teachings of this specification.

The following examples are included to illustrate procedures forpracticing the invention and to demonstrate certain preferredembodiments of the invention. These examples should not be construed aslimiting. It should be appreciated by those of skill in the art that thetechniques disclosed in the following examples represent specificapproaches used to illustrate preferred modes for its practice. However,those of skill in the art should, in light of the present disclosure,appreciate that many changes can be made in these specific embodimentswhile still obtaining like or similar results without departing from thespirit and scope of the invention. Unless otherwise indicated, allpercentages are by weight and all solvent mixture proportions are byvolume unless otherwise noted.

The following abbreviations are used unless otherwise indicated.

AAD-1 aryloxyalkanoate dioxygenase-1 bp base pair ° C. degrees CelciusDNA deoxyribonucleic acid DIG digoxigenin EDTAethylenediaminetetraacetic acid kb kilobase μg microgram μL microlitermL milliliter M molar mass OLP overlapping probe PCR polymerase chainreaction PTU plant transcription unit SDS sodium dodecyl sulfate SOPstandard operating procedure SSC a buffer solution containing a mixtureof sodium chloride and sodium citrate, pH 7.0 TBE a buffer solutioncontaining a mixture of Tris base, boric acid and EDTA, pH 8.3 V volts

EXAMPLES Example 1. Transformation and Selection of the AAD1 EventpDAS1740-278

The AAD1 event, pDAS1740-278, was produced by WHISKER-mediatedtransformation of maize line Hi-11. The transformation method used isdescribed in US Patent Application #20090093366. An FspI fragment ofplasmid pDAS1740, also referred to as pDAB3812, (FIG. 1) was transformedinto the maize line. This plasmid construct contains the plantexpression cassette containing the RB7 MARv3:: Zea mays Ubiquitin 1promoter v2//AAD1 v3//Zea mays PER5 3′UTR::RB 7 MARv4 planttranscription unit (PTU).

Numerous events were produced. Those events that survived and producedhealthy, haloxyfop-resistant callus tissue were assigned uniqueidentification codes representing putative transformation events, andcontinually transferred to fresh selection medium. Plants wereregenerated from tissue derived from each unique event and transferredto the greenhouse.

Leaf samples were taken for molecular analysis to verify the presence ofthe AAD-1 transgene by Southern Blot, DNA border confirmation, andgenomic marker assisted confirmation. Positive T0 plants were pollinatedwith inbred lines to obtain T1 seed. T1 plants of Event pDAS1470-278-9(DAS-40278-9) was selected, self-pollinated and characterized for fivegenerations. Meanwhile, the T1 plants were backcrossed and introgressedinto elite germplasm (XHH13) through marker-assisted selection forseveral generations. This event was generated from an independenttransformed isolate. The event was selected based on its uniquecharacteristics such as single insertion site, normal Mendeliansegregation and stable expression, and a superior combination ofefficacy, including herbicide tolerance and agronomic performance inbroad genotype backgrounds and across multiple environmental locations.The following examples contain the data which were used to characterizeevent pDAS-1740-278-9.

Example 2. pDAS1740-278-9 Event Characterization Via Southern Blot

Southern blot analysis was used to establish the integration pattern ofthe inserted DNA fragment and determine insert/copy number of the aad-1gene in event pDAS-1740-278-9 (DAS-40278-9). Data were generated todemonstrate the integration and integrity of the aad-1 transgeneinserted into the corn genome.

Southern blot data suggested that the pDAS1740/Fsp I fragment insert incorn event DAS-40278-9 occurred as a simple integration of a single,intact copy of the aad-1 PTU from plasmid pDAS 1740. Detailed Southernblot analysis was conducted using probes specific to gene, promoter,terminator, and other regulation elements contained in the plasmidregion and descriptive restriction enzymes that have cleavage siteslocated within the plasmid and produce hybridizing fragments internal tothe plasmid or fragments that span the junction of the plasmid with corngenomic DNA (border fragments). The molecular weights indicated from theSouthern hybridization for the combination of the restriction enzyme andthe probe were unique for the event, and established its identificationpatterns. These analyses also showed that the plasmid fragment had beeninserted into corn genomic DNA without rearrangements of the aad-1 PTU.Identical hybridization fragments were observed in five distinctgenerations of transgenic corn event DAS-40278-9 indicating stability ofinheritance of the aad-1 PTU insertion across generations. Hybridizationwith a mixture of three backbone probes located outside of therestriction site of Fsp I on plasmid pDAS 1740 did not detect anyspecific DNA/gene fragments, indicating the absence of the Ampicillinresistance gene and the absence of the other vector backbone regionsimmediately adjacent to the Fsp I restriction sites of the plasmid pDAS1740 in transgenic corn event DAS-40278-9. The illustrated map of theinsert in aad-1 corn event DAS-40278-9 is presented in FIGS. 2-3.

Example 2.1 Corn Leaf Sample Collection and Genomic DNA (gDNA) Isolation

gDNA prepared from leaf of the individual plants of the aad-1 corn eventDAS-40278-9. gDNA was extracted from leaf tissue harvested fromindividual plants carrying aad-1 corn event DAS-40278-9. Transgenic cornseeds from five distinct generations of event DAS-40278-9 were used.Twenty individual corn plants, derived from four plants per generation,for event DAS-40278-9 were selected. In addition, gDNA was isolated froma conventional corn plant, XHH13, which contains the genetic backgroundthat is representative of the substance line, absent the aad-1 gene.

Prior to isolating the gDNA, leaf punches were taken from each plant totest aad-1 protein expression using a rapid test strip kit (AmericanBionostica, Swedesboro, N.J.) according to the manufacturer'srecommended procedure. Each leaf punch sample was given a score of + or− for the presence or absence of aad-1, respectively. Only positiveplants from the five generations of event DAS-40278-9 were subjected tofurther characterization.

Corn leaf samples were collected from the individual plants of the eventDAS-40278-9 and the conventional control XHH13. Leaf samples werequickly frozen in liquid nitrogen and stored at approximately −80° C.until usage.

Individual genomic DNA was extracted from frozen corn leaf tissuefollowing the standard CTAB method. When necessary, some of the genomicDNA was further purified with Qiagen Genomic-Tip (Qiagen, Valencia,Calif.) following procedures recommended by the manufacturer. Followingextraction, the DNA was quantified spectrofluorometrically using PicoGreen reagent (Invitrogen, Carlsbad, Calif.). The DNA was thenvisualized on an agarose gel to confirm values from the Pico Greenanalysis and to determine the DNA quality.

Example 2.2 DNA Digestion and Separation

For molecular characterization of the DNA, nine micrograms (9 μg) ofgenomic DNA from the corn event DAS-40278-9 DNA sample and theconventional control were digested by adding approximately five toeleven units of selected restriction enzyme per μg of DNA and thecorresponding reaction buffer to each DNA sample. Each sample wasincubated at approximately 37° C. overnight. The restriction enzymesEcoR I, Nco I, Sac I, Fse I, and Hind III were used for the digests (NewEngland Biolabs, Ipswich, Mass.). A positive hybridization controlsample was prepared by combining plasmid DNA, pDAS1740 (pDAB3812), withgenomic DNA from the conventional control at a ratio of approximatelyequivalent to 1 copy of transgene per corn genome, and digested usingthe same procedures and restriction enzyme as the test samples. DNA fromthe conventional corn control (XHH13) was digested using the sameprocedures and restriction enzymes as the test samples to serve as anegative control.

The digested DNA samples were precipitated with Quick-Precip (EdgeBioSystems, Gaithersburg, Md.) and resuspended in 1× Blue Juice(Invitrogen, Carlsbad, Calif.) to achieve the desired volume for gelloading. The DNA samples and molecular size markers were thenelectrophoresed through 0.8% agarose gels with 1×TBE buffer (FisherScientific, Pittsburgh, Pa.) at 55-65 volts for approximately 18-22hours to achieve fragment separation. The gels were stained withethidium bromide (Invitrogen, Carlsbad, Calif.) and the DNA wasvisualized under ultraviolet (UV) light.

Example 2.3 Southern Transfer and Membrane Treatment

Southern blot analysis was performed essentially as described byMemelink, et al. (1994) Southern, Northern, and Western Blot Analysis.Plant Mol. Biol. Manual F1:1-23. Briefly, following electrophoreticseparation and visualization of the DNA fragments, the gels weredepurinated with 0.25N HCl (Fisher Scientific, Pittsburgh, Pa.) forapproximately 15 minutes, and then exposed to a denaturing solution(AccuGENE, Sigma, St. Louis, Mo.) for approximately 30 minutes followedby neutralizing solution (AccuGENE, Sigma, St. Louis, Mo.) for at least30 minutes. Southern transfer was performed overnight onto nylonmembranes (Roche Diagnostics, Indianapolis, Ind.) using a wicking systemwith 10×SSC (Sigma, St. Louis, Mo.). After transfer the membranes werewashed in a 2×SSC solution and the DNA was bound to the membrane by UVcrosslinking. This process resulted in Southern blot membranes ready forhybridization.

Example 2.4 DNA Probe Labeling and Hybridization

The DNA fragments bound to the nylon membrane were detected using alabeled probe. Probes used for the study were generated by a PCR-basedincorporation of a digoxigenin (DIG) labeled nucleotide, [DIG-11]-dUTP,from fragments generated by primers specific to gene elements and otherregions from plasmid pDAS 1740. Generation of DNA probes by PCRsynthesis was carried out using a PCR DIG Probe Synthesis Kit (RocheDiagnostics, Indianapolis, Ind.) following the manufacturer'srecommended procedures. A list of probes used for the study is describedin Table 1.

TABLE 1 Location and Length of Probes used in Southern Analysis. ProbePosition on Name Genetic Element pDAS1740 (bp) Length (bp) OLP1-3ubiquitin promoter (ZmUbi1)  28-2123 2096 OLP2 aad-1 gene 2103-3022 920OLP3A peroxidase terminator (ZmPer5) 3002-3397 396 OLP3B RB7 Mar v43375-4865 1491 OLP4ABC Backbone (OLP4A) 4900-5848 949 Backbone Ap^(r)gene (OLP4B) 5828-6681 855 Backbone (OLP4C) 6660-7144 485 OLP5-2 RB7 Marv3 7124-8507 1384

Labeled probes were analyzed by agarose gel electrophoresis to determinetheir quality and quantity. A desired amount of labeled probe was thenused for hybridization to the target DNA on the nylon membranes fordetection of the specific fragments using the procedures described forDIG Easy Hyb Solution (Roche Diagnostics, Indianapolis, Ind.). Briefly,nylon membrane blots with DNA fixed on were briefly washed in 2×SSC andprehybridized with 20-25 mL of prewarmed DIG Easy Hyb solution inhybridization bottles at approximately 50° C. for a minimal of 30minutes in a hybridization oven. The prehybridization solution were thendecanted and replaced with 20 mL of prewarmed DIG Easy Hyb solutioncontaining a desired amount of specific probes predenatured by boilingin water for 5 minutes. The hybridization step was then conducted atapproximately 40-60° C. overnight in the hybridization oven.

Example 2.5 Detection

At the end of the probe hybridization, DIG Easy Hyb solutions containingthe probes were decanted into clean tubes and stored at −20° C. Theseprobes could be reused for 2-3 times according to the manufacturer'srecommended procedure. The membrane blots were rinsed briefly and washedtwice in clean plastic containers with low stringency wash buffer(2×SSC, 0.1% SDS) for approximately 5 minutes at room temperature,followed by washing twice with high stringency wash buffer (0.1×SSC,0.1% SDS) for 15 minutes each at approximately 65° C. The membrane blotswere then transferred to other clean plastic containers and brieflywashed with 1× washing buffer from the DIG Wash and Block Buffer Set(Roche Diagnostics, Indianapolis, Ind.) for approximately 2 minutes,proceeded to blocking in 1× blocking buffer for a minimum of 30 minutes,followed by incubation with anti-DIG-AP (alkaline phosphatase) antibody(1:5,000 dilution, Roche Diagnostics, Indianapolis, Ind.) in 1× blockingbuffer for a minimum of 30 minutes. After 2-3 washes with 1× washingbuffer, specific DNA probes remain bound to the membrane blots andDIG-labeled DNA standards were visualized using CDP-StarChemiluminescent Nucleic Acid Detection System (Roche Diagnostics,Indianapolis, Ind.) following the manufacturer's recommendation. Blotswere exposed to chemiluminescent film (Roche Diagnostics, Indianapolis,Ind.) for one or more time points to detect hybridizing fragments and tovisualize molecular size standards. Films were then developed with anAll-Pro 100 Plus film developer (Konica SRX-101) and images were scannedfor report. The number and sizes of detected bands were documented foreach probe. DIG-labeled DNA Molecular Weight Marker II (MWM DIG II),visible after DIG detection as described, was used to determinehybridizing fragment size on the Southern blots.

Example 2.6 Probe Stripping

DNA probes were stripped off the membrane blots after the Southernhybridization data were obtained, and the membrane blots could be reusedfor hybridization with a different DNA probe according to themanufacturer's recommended procedures (DIG Application Manual for FilterHybridization, (2003). Roche Diagnostics). Briefly, after signaldetection and film exposure, membrane blots were thoroughly rinsed withMilli-Q water and followed by washing twice in stripping buffer (0.2NNaOH, 0.1% SDS) for approximately 15 minutes at room temperature or at37° C. The membrane blots were then briefly washed in 2×SSC and wereready for prehybridization and hybridization with another DNA probe. Themembrane blots were exposed to a new chemiluminescent film to ensure allthe DNA probes were stripped of before proceeding to the nexthybridization. The re-exposed films were kept along with the previoushybridization data package in the study file for record.

Example 2.7 Southern Blot Results

Expected and observed fragment sizes with a particular digest and probe,based on the known restriction enzyme sites of the pDAS1740/Fsp Ifragment, are given in Table 2. Two types of fragments were identifiedfrom these digests and hybridizations: internal fragments, where knownenzyme sites flank the probe region and are completely contained withinthe pDAS1740/Fsp I fragment and border fragments where a known enzymesite is located at one end of the probe region and a second site isexpected in the corn genome. Border fragment sizes vary by eventbecause, in most cases, DNA fragment integration sites are unique foreach event. The border fragments provide a means to locate a restrictionenzyme site relative to the integrated DNA and to evaluate the number ofDNA insertions. Based on the Southern blot analyses completed in thisstudy, it was concluded that a single copy of an intact aad-1 PTU fromplasmid pDAS1740/Fsp I inserted into the corn genome of eventDAS-40278-9 as detailed in the insert map (FIGS. 2-3).

TABLE 2 Predicted and Observed Hybridizing Fragments in Southern BlotAnalysis. Expected Observed DNA Restriction Fragment Fragment Size ProbeEnzymes Sizes (bp) ¹ (bp)2 aad-1 EcoR I pDAS1740 8512   8512 XHH13 nonenone DAS-40278-9 >3382 (border) ~12000  Nco I pDAS1740 8512   8512 XHH13none none DAS-40278-9 >2764 (border) ~4000 Sac I pDAS1740 8512   8512XHH13 none none DAS-40278-9 >4389 (border) ~16000  Fse I/Hind pDAS17403361   3361 III XHH13 none none DAS-40278-9 3361   3361 ZmUbi1 Nco IpDAS1740 8512 8512, ~3600* prom. XHH13 none  ~3600* DAS-40278-9 >3472(border) ~6300, ~3600* Sac I pDAS1740 8512 8512, ~3800* XHH13 none ~3800* DAS-40278-9 >4389 (border) ~3800*, ~16000 Fse I/Hind pDAS17403361 3361, ~6400* III XHH13 none  ~6400* DAS-40278-9 3361 3361, ~6400*#ZmPer5 Nco I pDAS1740 8512 8512, −3900* term. XHH13 none  −3900*DAS-40278-9 >2764 (border) −4000, −3900* Sac I pDAS1740 8512 8512,−9000* XHH13 none  −9000* DAS-40278-9 >1847 (border) −1900, −9000* FseI/Hind pDAS1740 3361 3361, −2100* III XHH13 none  −2100* DAS-40278-93361 3361, −2100* RB7 Nco I pDAS1740 8512   8512 mar4 XHH13 none noneDAS-40278-9 >2764 (border) −4000 >3472 (border) −6300 Sac I pDAS17408512   8512 XHH13 none none DAS-40278-9 >1847 (border) −1900 >4389(border) −16000  RB7 Nco I pDAS1740 8512   8512 mar3 XHH13 none noneDAS-40278-9 >2764 (border) −4000 >3472 (border) −6300 Sac I pDAS17408512   8512 XHH13 none none DAS-40278-9 >1847 (border) −1900 >4389(border) −16000  backbone Nco I pDAS1740 8512   8512 XHH13 none noneDAS-40278-9 none none Sac I pDAS1740 8512 8512 XHH13 none noneDAS-40278-9 none none Note: *An asterisk after the observed fragmentsize indicates endogenous sequence hybridization that was detectedacross all samples (including negative controls) #Doublets in theconventional control, BC3S1, and some BC3S2 samples as shown ¹ Expectedfragment sizes are based on the plasmid map of the pDAS1740 (pDAB3812)in FIG. 1 2Observed fragment sizes are considered approximately fromthese analyses and are based on the indicated sizes of the DIG-labeledDNA Molecular Weight Marker II fragments. Due to the incorporation ofDIG molecules for visualization, the marker fragments typically runapproximately 5-10% larger than their actual indicated molecular weight.

Restriction enzymes with unique restriction site in plasmid pDAS 1740,EcoR I, Nco I, Sac I, Fse I/Hind III, were selected to characterizeaad-1 gene insert in event DAS-40278-9. Border fragment of >3382bp, >2764 bp, >4389 bp was predicted to hybridize with the aad-1 geneprobe following EcoR I, Nco I, and Sac I digest respectively (Table 2).Single aad-1 hybridization band of ˜12000 bp, ˜4000 bp, and ˜16000 bpwere observed when EcoR I, Nco I, and Sac I were used respectively,indicating a single site of aad-1 gene insertion in the corn genome ofevent DAS-40278-9. Double digestion with Fse I and Hind III was selectedto release a fragment of 3361 bp which contains the aad-1 planttranscription unit (PTU, promoter/gene/terminator) (Table 2). Thepredicted 3361 bp fragment was observed with the aad-1 gene probefollowing Fse I/Hind III digestion. Results obtained with all fourenzymes/enzyme combination digestion of the DAS-40278-9 sample followedby aad-1 gene probe hybridization indicated that a single copy of anintact aad-1 PTU from plasmid pDAS 1740 was inserted into the corngenome of event DAS-40278-9.

Restriction enzymes Nco I, Sac I and Fse I/Hind III were selected tocharacterize the promoter (ZmUbil) region for aad-1 in eventDAS-40278-9. Nco I and Sac I digests are expected to generate a borderregion fragment of >3472 bp and >4389 bp, respectively, when hybridizedto DNA probes specifically to the ZmUbil promoter region (Table 2). Twohybridization bands of ˜6300 bp and ˜3600 bp were detected with ZmUbilpromoter probe following Nco I digestion. The ˜3600 bp band, however,was present across all sample lanes including the conventional controls,suggesting that the ˜3600 bp band is a non-specific signal bandresulting from the homologous binding of the corn-derived ubiquitinpromoter (ZmUbil) probe to the corn endogenous ubi gene. On thecontrary, the ˜6300 bp signal band was detected in the testedDAS-40278-9 samples but not in the conventional controls, indicatingthat the ˜6300 bp band is specific to the ZmUbil promoter probe fromplasmid pDAS1740 and therefore it is the expected Nco I/ZmUbil bandindicated in Table 2. Similarly, two hybridization bands of ˜3800 bp and˜16000 bp were detected with ZmUbil promoter probe following Sac Idigestion. The ˜3800 bp band appeared in all sample lanes includingconventional controls and thus is considered as non-specifichybridization of ZmUbil promoter probe to the corn endogenous ubi gene.The ˜16000 bp hybridization band that is only present in DAS-40278-9samples is considered the expected Sac I/ZmUbil band. Double digestionwith Fse I/Hind III is expected to release the aad-1 PTU fragment of3361 bp that hybridizes to the ZmUbil promoter probe (Table 2). This3361 bp band and a non-specific hybridization band of ˜6400 bp weredetected by ZmUbil promoter probe following Fse I/Hind III digestion.The ˜6400 bp band is considered non-specific binding of the ZmUbilpromoter probe to the corn endogenous ubi gene because this band ispresent in all sample lanes including the conventional controls.Additionally, another band very close to ˜6400 bp was observed in theconventional control, BC3S1, and some of the BC3S2 samples. Thisadditional band very close to ˜6400 bp is also considered non-specificbecause it is present in the conventional control XHH13 sample lanes andis most likely associated with the genetic background of XHH13.

The same restriction enzymes/enzyme combination, Nco I, Sac I and FseI/Hind III were selected to characterize the terminator (ZmPer5) regionfor aad-1 in event DAS-40278-9. Nco I digest is expected to generate aborder region fragment of >2764 bp when hybridized to DNA probesspecifically to the ZmPer5 terminator region (Table 2). Twohybridization bands of ˜4000 bp and ˜3900 bp were detected with ZmPer5terminator probe following Nco I digestion. The ˜3900 bp band waspresent across all sample lanes including the conventional controls,suggesting that the ˜3900 bp band is a non-specific signal band probablydue to the homologous binding of the corn-derived peroxidase geneterminator (ZmPer5) probe to the corn endogenous per gene. On thecontrary, the ˜4000 bp signal band was detected in the testedDAS-40278-9 samples but not in the conventional controls, indicatingthat the ˜4000 bp band is specific to the ZmPer5 terminator probe fromplasmid pDAS 1740 and therefore it is the expected Nco I/ZmPer5 bandindicated in Table 2. A >1847 bp border fragment is expected tohybridized to the ZmPer5 terminator probe following Sac I digestion. Twohybridization bands of ˜1900 bp and ˜9000 bp were detected with ZmPer5terminator probe following Sac I digestion. The ˜9000 bp band appearedin all sample lanes including conventional controls and thus consideredas non-specific hybridization of ZmPer5 terminator probe to the cornendogenous per gene. The ˜1900 bp hybridization band that was onlypresent in DAS-40278-9 samples is considered the expected Sac I/ZmPer5band. Double digestion with Fse I/Hind III is expected to release theaad-1 PTU fragment of 3361 bp that hybridizes to the ZmPer5 terminatorprobe (Table 2). This 3361 bp band and an additional non-specifichybridization band of ˜2100 bp were detected by ZmPer5 terminator probefollowing Fse I/Hind III digestion. The additional ˜2100 bp band is thenon-specific binding of the ZmPer5 terminator probe to the cornendogenous gene since this band is present in all sample lanes includingthe negative controls. Results obtained with these digestions of theDAS-40278-9 sample followed by ZmUbil promoter and ZmPer5 terminatorprobe hybridization further confirmed that a single copy of an intactaad-1 PTU from plasmid pDAS 1740 was inserted into the corn genome ofevent DAS-40278-9.

Restriction enzymes, Nco I and Sac I, were selected to characterize therest of the components from pDAS1740/Fsp I fragment in AAD-1 corn eventDAS-40278-9 (Table 2). DNA sequences of components RB7 Mar v3 and RB7Mar v4 have over 99.7% identity, therefore DNA probes specific for RB7Mar v3 or RB7 Mar v4 were expected to hybridize to DNA fragmentscontaining either version of the RB7 Mar. Two border fragments of >2764bp and >3472 bp were expected to hybridize with RB7 Mar v4 and RB7 Marv3 probes following Nco I digestion (Table 2). Two hybridization bandsof ˜4000 bp and ˜6300 bp were observed with either RB7 Mar v4 or RB7 Marv3 probe after Nco I digestion in DAS-40278-9 samples. Similarly, twoborder fragments of >1847 bp and >4389 bp were predicted with RB7 Mar v4and RB7 Mar v3 probes following Sac I digestion (Table 2). Hybridizationbands of ˜1900 bp and ˜16000 bp were detected in DAS-40278-9 sampleswith RB7 Mar v4 or RB7 Mar v3 probe after Sac I digestion.

Taken together, the Southern hybridization results obtained with theseelement probes indicated that the DNA inserted in corn event DAS-40278-9contains an intact aad-1 PTU along with the matrix attachment regionsRB7 Mar v3 and RB7 Mar v4 at the 5′ and 3′ ends of the insert,respectively.

Example 2.8 Absence of Backbone Sequences

Equal molar ratio combination of three DNA fragments (Table 1) coveringnearly the entire Fsp I backbone region (4867-7143 bp in plasmid pDAS1740) of plasmid pDAS 1740 were used as the backbone probe tocharacterize AAD-1 corn event DAS-40278-9. Plasmid pDAS 1740/Fsp Ifragment was used to generate event DAS-40278-9, therefore, no specifichybridization signal was expected with the backbone probe combination(Table 2) following any restriction enzyme digestion. It was confirmedthat no specific hybridization signal was detected with backbone probefollowing Nco I or Sac I digestion in all DAS-40278-9 samples. Positivecontrol lanes contained the expected hybridizing bands demonstratingthat the probes were capable of hybridizing to any homologous DNAfragments if present in the samples. The data suggested that theinsertion in corn event DAS-40278-9 did not include any vector backbonesequence outside of the Fsp I region from plasmid pDAS 1740.

Leaf samples from five distinct generations of the event DAS-40278-9were used to conduct the Southern blot analysis for molecularcharacterization. The integration pattern was investigated usingselected restriction enzyme digest and probe combinations tocharacterize the inserted gene, aad-1, as well as the non-coding regionsincluding promoter, terminator of gene expression, and the matrixattachment regions.

Southern blot characterization of the DNA inserted into eventDAS-40278-9 indicate that a single intact copy of the aad-1 PTU has beenintegrated into event DAS-40278-9. The molecular weights indicated bythe Southern hybridization for the combination of the restriction enzymeand the probe were unique for the event, and established itsidentification patterns. The hybridization pattern is identical acrossall five generations, indicating that the insert is stable in the corngenome. Hybridization with probes covering the backbone region beyondthe pDAS1740/Fsp I transformation fragment from plasmid pDAS1740confirms that no vector backbone sequences have been incorporated intothe event DAS-40278-9.

Example 3. Cloning and Characterization of DNA Sequence in the Insertand the Flanking Border Regions of Corn Event DAS-40278-9

To characterize the inserted DNA and describe the genomic insertionsite, DNA sequences of the insert and the border regions of eventDAS-40278-9 were determined. In total, 8557 bp of event DAS-40278-9genomic sequence were confirmed, comprising 1873 bp of 5′ flankingborder sequence, 1868 bp of 3′ flanking border sequence, and 4816 bp ofDNA insert. The 4816 bp DNA insert contains an intact aad-1 expressioncassette, a 259 bp partial MAR v3 on the 5′ terminus, and a 1096 bppartial MAR v4 on the 3′ terminus. Sequence analysis revealed a 21 bpinsertion at 5′-integration junction and a two base pair deletion fromthe insertion locus of the corn genome. A one base pair insertion wasfound at 3′-integration junction between the corn genome and theDAS-40278-9 insert. Also, a single base change (T to C) was found in theinsert at position 5212 in the non-coding region of the 3′ UTR. None ofthese changes affect the open reading frame composition of the aad-1expression cassette.

PCR amplification based on the event DAS-40278-9 insert and bordersequences confirmed that the border regions were of corn origin and thatthe junction regions could be used for event-specific identification ofDAS-40278-9. Analysis of the sequence spanning the junction regionsindicated that no novel open reading frames (ORF>=200 codons) resultedfrom the DNA insertion in event DAS-40278-9 and also no genomic openreading frames were interrupted by the DAS-40278-9 integration in thenative corn genome. Overall, characterization of the insert and bordersequences of the AAD-1 corn event DAS-40278-9 indicated that a singleintact copy of the aad-1 expression cassette was integrated into thenative corn genome.

Example 3.1 Genomic DNA Extraction and Quantification

Genomic DNA was extracted from lyophilized or freshly ground leaftissues using a modified CTAB method. DNA samples were dissolved in 1×TE(10 mM Tris pH8.0, 1 mM EDTA) (Fluka, Sigma, St. Louis, Mo.) andquantified with the Pico Green method according to manufacturer'sinstructions (Molecular Probes, Eugene, Oreg.). For PCR analysis, DNAsamples were diluted with molecular biology grade water (5 PRIME,Gaithersburg, Md.) to result in a concentration of 10-100 ng/μL.

Example 3.2 PCR Primers

Table 3 lists the primer sequences that were used to clone the DNAinsert and the flanking border regions of event DAS-40278-9, withpositions and descriptions marked in FIG. 4. Table 4 lists the primersequences that were used to confirm the insert and border sequences. Theprimer positions were marked in FIGS. 4 and 5, respectively. All primerswere synthesized by Integrated DNA Technologies, Inc. (Coralville,Iowa). Primers were dissolved in water (5 PRIME, Gaithersburg, Md.) to aconcentration of 100 μM for the stock solution and diluted with water toa concentration of 10 μM for the working solution.

TABLE 3List of primer sequences used in the cloning of the insert in Corn Event DAS-40278-9and flanking border sequence. Size Location Primer Name (bp) (bp)Sequence Purpose 5End3812_A 26 2231-2256 (-) Seq ID No: 1: 5′Primary PCR for 5′ TGCACTGCAGGTCGACTCTAGAGGAT-3′ border sequence5End3812_B 23 2110-2132 (-) Seq ID No: 2: 5′- Second PCR for 5′GCGGTGGCCACTATTTTCAGAAG-3′ border sequence 3End3812_C 26 5535-5560 (+)Seq ID No: 3: 5′- Primary PCR for 3′ TTGTTACGGCATATATCCAATAGCGG-3′border sequence 3End3812_D 26 5587-5612 (+) Seq ID No: 4: 5′-Secondary PCR for 3′ CCGTGGCCTATTTTCAGAAGAAGTTC-3′ border sequenceAmp 1F 23 736-758 (+) Seq ID NO: 5: 5′- Amplification of theACAACCATATTGGCTTTGGCTGA-3′ insert, Amplicon 1, used with Amp 1R Amp 1R28 2475-2502 (-) Seq ID NO: 6: Amplification of the5′CCTGTTGTCAAAATACTCAATTGTCCTT- insert, Amplicon 1, 3′ used with Amp 1FAmp 2F 23 1696-1718 (+) Seq ID NO: 7: 5′- Amplification of theCTCCATTCAGGAGACCTCGCTTG-3′ insert, Amplicon 2, used with Amp 2R Amp 2R23 3376-3398 (-) Seq ID NO: 8: Amplification of the5′GTACAGGTCGCATCCGTGTACGA-3′ insert, Amplicon 2, used with Amp 2F Amp 3F25 3254-3278 (+) Seq ID NO: 9: 5′- Amplification of theCCCCCCCTCTCTACCTTCTCTAGAT-3′ insert, Amplicon 3, used with Amp 3R Amp 3R23 4931-4953 (-) Seq ID NO: 10: 5′- Amplification of theGTCATGCCCTCAATTCTCTGACA-3′ insert, Amplicon 3, used with Amp 3F Amp 4F23 4806-4828 (+) Seq ID NO: 11: 5′- Amplification of theGTCGCTTCAGCAACACCTCAGTC-3′ insert, Amplicon 4 used with Amp 4R Amp 4R 236767-6789 (-) Seq ID NO: 12: 5′- Amplification of theAGCTCAGATCAAAGACACACCCC-3′ insert, Amplicon 5, used with Amp 5F Amp 5F28 6300-6327 (+) Seq ID NO: 13: 5′- Amplification of theTCGTTTGACTAATTTTTCGTTGATGTAC-3′ insert, Amplicon 5, used with Amp 5RAmp 5R 23 7761-7783 (-) Seq ID NO: 14: 5′- Amplification of theTCTCACTTTCGTGTCATCGGTCG-3′ insert, Amplicon 5, used with Amp 5F (+):Direct sequence; (-): Complementary sequence;

TABLE 4List of primer sequences used in the confirmation of corn genomic DNASize Location Primer Name (bp) (bp) Sequence Purpose 1F5End01 171816-1832 (+) Seq ID NO: 15: 5′- Confirmation of 5′ borderCCAGCACGAACCATTGA-3′ genomic DNA, used with A15End01 1F5End02 241629-1652 (+) Seq ID NO: 16: 5′- Confirmation of 5′ borderCGTGTATATAAGGTCCAGAGGGTA- genomic DNA, used with 3′ A15End02 A15End01 174281-4297 (-) Seq ID NO: 17: 5′- Confirmation of 5′ borderTTGGGAGAGAGGGCTGA-3′ genomic DNA, used with 1F5End01 A15End02 204406-4426 (-) Seq ID NO: 18: 5′- Confirmation of 5′ borderTGGTAAGTGTGGAAGGCATC-3′ genomic DNA, used with 1F5End02 1F3End03 208296-8315 (-) Seq ID NO: 19: 5′- Confirmation of genomicGAGGTACAACCGGAGCGTTT-3′ DNA, used with 1F5End03 1F3End04 198419-8437 (-) Seq ID NO: 20: 5′- Confirmation of genomicCCGACGCTTTTCTGGAGTA-3′ DNA, used with 1F5End04 1F5End03 22 378-399 (+)Seq ID NO: 21: 5′- Confirmation of genomic TGTGCCACATAATCACGTAACA-3′DNA, used with 1F3End03 1F5End04 20 267-286 (+) Seq ID NO: 22: 5′-Confirmation of genomic GAGACGTATGCGAAAATTCG-3′ DNA, used with 1F3End04A13End01 22 4973-4994 (+) Seq ID NO: 23: 5′- Confirmation of 3′ borderTTGCTTCAGTTCCTCTATGAGC-3′ genomic DNA, used with 1F3End05 1F3End 05 197060-7078 (-) Seq ID NO: 24: 5′- Confirmation of 3′ borderTCCGTGTCCACTCCTTTGT-3′ genomic DNA, used with A13End01 1F5End T1F 222033-2054 (-) Seq ID NO: 25: 5′- 278 specific sequenceGCAAAGGAAAACTGCCATTCTT-3′ amplification at 5′ junction 1F5EndT1R 201765-1784 (+) Seq ID NO: 26: 5′- 278 specific sequenceTCTCTAAGCGGCCCAAACTT-3′ amplification at 5′ junction Corn278-F 231884-1906 (-) Seq ID NO: 27: 5′- 278 specific sequenceATTCTGGCTTTGCTGTAAATCGT-3′ amplification at 5′ junction Corn278-R 241834-1857 (+) Seq ID NO: 28: 5′- 278 specific sequenceTTACAATCAACAGCACCGTACCTT amplification at 5′ junction (+): Directsequence; (-): Complementary sequence;

Example 3.3. Genome Walking

The GenomeWalker™ Universal Kit (Clontech Laboratories, Inc., MountainView, Calif.) was used to clone the 5′ and 3′ flanking border sequencesof corn event DAS-40278-9. According to the manufacturer's instruction,about 2.5 μg of genomic DNA from AAD-1 corn event DAS-40278-9 wasdigested overnight with EcoR V, Stu I (both provided by the kit) or ScaI (New England Biolabs, Ipswich, Mass.). Digested DNA was purified usingthe DNA Clean & Concentrator™-25 (ZYMO Research, Orange, Calif.)followed by ligation to GenomeWalker™ adaptors to constructGenomeWalker™ libraries. Each GenomeWalker™ library was used as DNAtemplate for primary PCR amplification with the adaptor primer AP1,provided in the kit, and each construct-specific primer 5End3812_A and3End3812_C. One microliter of 1:25 dilution of primary PCR reaction wasthen used as template for secondary PCR amplification with the nestedadaptor primer AP2 and each nested construct-specific primer 5End3812_Band 3End3812_D. TaKaRa LA Taq™ HS (Takara Bio Inc., Shiga, Japan) wasused in the PCR amplification. In a 50 μL PCR reaction, 1 μL of DNAtemplate, 8 μL of 2.5 mM of dNTP mix, 0.2 μM of each primer, 2.5 unitsof TaKaRa LA Taq™ HS DNA Polymerase, 5 μl of 10×LA PCR Buffer II (Mg2+plus), and 1.5 μL of 25 mM MgCl₂ were used. Specific PCR conditions arelisted in Table 5.

TABLE 5 Conditions for Genome Walking of the AAD-1 Corn EventDAS-40278-9 to Amplify the Flanking Border Regions Pre- Final denatureDenature Anneal Extension Denature Anneal Extension Extension Target (°C./ (° C./ (° C./ (° C./ (° C./ (° C./ (° C./ (° C./ Sequence Primer Setmin) sec.) sec.) min:sec) sec.) sec.) min:sec) min) 5′ border5End3812_A/ 95/3 95/30 68^(−0.5/cycle)→64/30 68/10:00 95/30 64/3068/10:00 72/10 AP1 8 cycles 22 cycles 5End3812_B/ 95/3068^(−0.5/cycle)→64/30 68/10:00 95/30 64/30 68/10:00 AP2 8 cycles 22cycles 3′ border 3End3812_C/ 95/3 95/30 68^(−0.5/cycle)→64/30 68/10:0095/30 64/30 68/10:00 72/10 AP1 8 cycles 22 cycles 3′ border 3End3812_D/95/3 95/30 68^(−0.5/cycle)→64/30 68/10:00 95/30 64/30 68/10:00 72/10(nested) AP2 8 cycles 22 cycles

Example 3.4. Conventional PCR

Standard PCR was used to clone and confirm the DNA insert and bordersequence in the corn event DAS-40278-9. TaKaRa LA Taq™ (Takara Bio Inc.,Shiga, Japan), HotStarTaq DNA Polymerase (Qiagen, Valencia, Calif.),Expand High Fidelity PCR System (Roche Diagnostics, Inc., Indianapolis,Ind.), or the Easy-A® High-Fidelity PCR Cloning Enzyme & Master Mix(Stratagene, LaJolla, Calif.) was used for conventional PCRamplification according to the manufacturer's recommended procedures.Specific PCR conditions and amplicon descriptions are listed in Table 6.

TABLE 6 Conditions for Standard PCR Amplification of the Border Regionsin the Corn Event DAS-40278-9 Pre- Final denature Denature AnnealExtension Extension Target Primer (° C./ (° C./ (° C./ (° C./ (° C./Sequence Set min) sec.) sec.) min:sec) min) 5′ border 1F5End01/ 95/395/30 60/30 68/5:00 72/10 AI5End01 35 cycles 5′ border 1F5End02/ 95/395/30 60/30 68/5:00 72/10 AI5End02 35 cycles Across the 1F3End03/ 95/395/30 60/30 68/5:00 72/10 insert locus 1F5End03 35 cycles Across the1F3End04/ 95/30 60/30 68/5:00 72/10

1F5End04 35 cycles 5′ junction Amp 1F/ 95/2 94/60 55/60 72/2:00 72/10(Amplicon 1) Amp 1R 35 cycles Amplicon 2 Amp 1F/ 95/2 94/60 55/6072/2:00 72/10 Amp 1R 35 cycles Amplicon 3 Amp 1F/ 95/2 94/60 55/6072/2:00 72/10 Amp 1R 35 cycles Amplicon 4 Amp 1F/ 95/2 94/60 55/6072/2:00 72/10 Amp 1R 35 cycles 3′ junction Amp 1F/ 95/2 94/60 55/6072/2:00 72/10 (Amplicon 5) Amp 1R 35 cycles 3′ border 1F3End05/ 95/395/30 60/30 68/5:00 72/10 A13End01 35 cycles

indicates data missing or illegible when filed

Example 3.5 PCR Product Detection, Purification, Sub-Cloning of PCRProducts, and Sequencing

PCR products were inspected by electrophoresis using 1.2% or 2% E-gel(Invitrogen, Carlsbad, Calif.) according to the product instruction.Fragment size was estimated by comparison with the DNA markers. Ifnecessary, PCR fragments were purified by excising the fragments from 1%agarose gel in 1×TBE stained with ethidium bromide, using the QiAquickGel Extraction Kit (Qiagen, Carlsbad, Calif.).

PCR fragments were sub-cloned into the pCR®4-TOPO® using TOPO TACloning® Kit for Sequencing (Invitrogen, Carlsbad, Calif.) according tothe product instruction. Specifically, two to five microliters of theTOPO® cloning reaction was transformed into the One Shot chemicallycompetent TOP10 cells following the manufacturer's instruction. Clonedfragments were verified by minipreparation of the plasmid DNA (QIAprepSpin Miniprep Kit, Qiagen, Carlsbad, Calif.) followed by restrictiondigestion with EcoR I or by direct colony PCR using T3 and T7 primers,provided in the kit. Plasmid DNA or glycerol stocks of the selectedcolonies were then sent for sequencing.

After sub-cloning, the putative target PCR products were sequencedinitially to confirm that the expected DNA fragments had been cloned.The colonies containing appropriate DNA sequences were selected forprimer walking to determine the complete DNA sequences. Sequencing wasperformed by Cogenics (Houston, Tex.).

Final assembly of insert and border sequences was completed usingSequencher software (Version 4.8 Gene Codes Corporation, Ann Arbor,Mich.). Annotation of the insert and border sequences of corn eventDAS-40278-9 was performed using the Vector NTI (Version 10 and 11,Invitrogen, Carlsbad, Calif.).

Homology searching was done using the BLAST program against the GenBankdatabase. Open reading frame (ORF) analysis using Vector NTI (Version11, Invitrogen) was performed to identify ORFs (>=200 codons) in thefull insert and flanking border sequences.

Example 3.6 5′ End Border Sequence

A DNA fragment was amplified from each corn event DAS-40278-9GenomeWalker™ library using the specific nested primer set for 5′ end ofthe transgene. An approximately 800 bp PCR product was observed fromboth the event DAS-40278-9 EcoR V and Stu I GenomeWalker™ libraries. TheSca I GenomeWalker™ library generated a product around 2 kb. Thefragments were cloned into pCR® 4-TOPO and six colonies from eachlibrary were randomly picked for end sequencing to confirm the insertcontained the expected sequences. Complete sequencing by primer walkingof the inserts revealed that the fragments amplified from corn eventDAS-40278-9 Stu I, EcoR V, and Sca I GenomeWalker™ libraries were 793,822, and 2132 bp, respectively. The DNA fragments generated from the StuI and EcoR V GenomeWalker™ libraries were a 100% match to the DNAfragment generated from Sca GenomeWalker™ library, suggesting that theseDNA fragments were amplified from the 5′ region of the transgene insert.BLAST search of the resultant 1873 bp corn genomic sequence indicated ahigh similarity to the sequence of a corn BAC clone. Moreover, sequenceanalysis of the insertion junction indicated that 917 bp of the MAR v3at its 5′ end region was truncated compared to the plasmid pDAS1740/FspI fragment, leaving a 259 bp partial MAR v3 at the 5′ region of theaad-1 expression cassette.

Example 3.7 3′ End Border Sequence

A DNA fragment with size of approximately 3 kb was amplified from cornevent DAS-40278-9 Stu I GenomeWalker™ library using the specific nestedprimer set for the 3′ end of the transgene. The DNA fragment was clonedinto pCR®4-TOPO® and ten colonies were randomly picked for endsequencing to confirm the insertion of the expected sequences. Threeclones with the expected inserts were completely sequenced, generating a2997 bp DNA fragment. Sequence analysis of this DNA fragment revealed apartial MAR v4 element (missing 70 bp of its 5′ region) and 1867 bp corngenomic sequence. BLAST search showed the 1867 bp genomic DNA sequencewas a 100% match to sequence in the same corn BAC clone as wasidentified with the 5′ border sequence.

Example 3.8 DNA Insert and Junction Sequence

The DNA insert and the junction regions were cloned from corn eventDAS-40278-9 using PCR based methods as previously described. Five pairsof primers were designed based on the 5′ and 3′ flanking bordersequences and the expected transgene sequence. In total, fiveoverlapping DNA fragments (Amplicon 1 of 1767 bp, Amplicon 2 of 1703 bp,Amplicon 3 of 1700 bp, Amplicon 4 of 1984 bp, and Amplicon 5 of 1484 bp)were cloned and sequenced (FIG. 4). The whole insert and flanking bordersequences were assembled based on overlapping sequence among the fivefragments. The final sequence confirms the presence of 4816 bp of theDNA insert derived from pDAS1740/Fsp I, 1873 bp of the 5′ flankingborder sequence, and 1868 bp of 3′ flanking border sequence. The 4816 bpDNA insert contains an intact aad-1 expression cassette, a 259 bppartial MAR v3 on the 5′ terminus, and a 1096 bp partial MAR v4 on the3′ terminus (Seq ID No: 29).

At least two clones for each primer pair were used for primer walking inorder to obtain the complete sequence information on the DNA insert andits border sequences. Sequence analysis indicated a 21 bp insertion at5′-integration junction between corn genome DNA and the integratedpartial MAR v3 from the pDAS1740/Fsp I. BLAST search and Vector NTIanalysis results indicated that the 21 bp insert DNA did not demonstratehomology to any plant species DNA or the pDAS1740 plasmid DNA. A singlebase pair insertion was found at the 3′-integration junction betweencorn genome DNA and the partial MAR v4 from the pDAS 1740/Fsp I. DNAintegration also resulted in a two base pair deletion at the insertionlocus of the corn genome (FIG. 6). In addition, one nucleotidedifference (T to C) at the position of 5212 bp was observed in thenon-translated 3′ UTR region of the DNA insert (Seq ID No: 29). However,none of these changes seem to be critical to aad-1 expression or createany new ORFs (>=200 codons) across the junctions in the insert ofDAS-40278-9.

Example 3.9 Confirmation of Corn Genomic Sequences

To confirm the insertion site of event DAS-40278-9 transgene in the corngenome, PCR amplification was carried out with different pairs ofprimers (FIG. 4). Genomic DNA from event DAS-40278-9 and othertransgenic or non-transgenic corn lines was used as a template. Twoaad-1 specific primers, A15End01 and A15End02, and two primers designedaccording to the 5′ end border sequence, 1F5End01 and 1F5End02, wereused to amplify DNA fragments spanning the aad-1 gene to 5′ end bordersequence. Similarly, to amplify a DNA fragment spanning the aad-1 to 3′end border sequence, 1F3End05 primer derived from the 3′ end bordersequence and aad-1 specific AI3End01 primer were used. DNA fragmentswith expected sizes were amplified only from the genomic DNA of AAD-1corn event DAS-40278-9, with each primer pair consisting of one primerlocated on the flanking border of AAD-1 corn event DAS-40278-9 and oneaad-1 specific primer. The control DNA samples did not yield PCRproducts with the same primer pairs indicating that the cloned 5′ and 3′end border sequences are indeed the upstream and downstream sequence ofthe inserted aad-1 gene construct, respectively. It is noted that afaint band with size of about 8 kb was observed in all the corn samplesincluding AAD-1 corn event DAS-40278-9, AAD-1 corn event DAS-40474 andnon transgenic corn line XHH13 when the primer pair of 1F5End01 andAI5End01 were used for PCR amplification. An observed faint band (on aprepared gel) could be a result of nonspecific amplification in corngenome with this pair of primers.

To further confirm the DNA insertion in the corn genome, two primerslocated at the 5′ end border sequence, 1F5End03 and 1F5End04, and twoprimers located at the 3′ end border sequence, 1F3End03 and 1F3End04,were used to amplify DNA fragments spanning the insertion locus. PCRamplification with either the primer pair of 1F5End03/1F3End03 or theprimer pair of 1F5End04/1F3End04 resulted in a fragment with expectedsize of approximately 8 kb from the genomic DNA of AAD-1 corn eventDAS-40278-9. In contrast, no PCR products resulted from the genomic DNAof AAD-1 corn event DAS-40474-7 or the non-transgenic corn line XHH13.Given that AAD-1 corn event DAS-40278-9 and event DAS-40474-7 weregenerated by transformation of Hill, followed by backcrossing theoriginal transgenic events with the corn line XHH13, the majority ofgenome in each of these two events is theoretically from the corn lineXHH13. It is very likely that only the flanking border sequences closeto the aad-1 transgene are carried over from the original genomic DNAand preserved during the AAD-1 event introgression process, while otherregions of genome sequences might have been replaced by the genomesequences of XHH13. Therefore, it is not surprising that no fragmentswere amplified from the genomic DNA of AAD-1 corn event DAS-40474-7 andXHH13 with either the primer pair of 1F5End03/1F3End03 or the primerpair of 1F5End04/1F3End04. Approximately 3.1 and 3.3 kb fragments wereamplified with the primer pair of 1F5End03/1F3End03 and1F5End04/1F3End04 respectively in the genomic DNA of the corn lines Hilland B73 but not in the corn line A188. The results indicate that theborder sequences originated from the genome of the corn line B73.

Additional cloning of corn genomic DNA from B73/HiII was performed toensure validity of the flanking border sequences. The PCR amplifiedfragments were sequenced in order to prove the insert DNA regionintegrated into the specific location of B73/HiII genomic DNA. Primerswere designed based on the sequence obtained. Primer set Amp 1F/Amp 5Rwas used to amplify a 2212 bp fragment spanning the 5′ to 3′ junctionsfrom native B73/HiII genome without insert DNA. Sequence analysisrevealed that there was a two base pair deletion from the native B73genome in the transgene insertion locus. Analysis of the DNA sequencesfrom the cloned native B73 genomic fragment identified one ORF (>=200codons) located downstream of the 3′-integration junction region.Additionally, there are no other ORFs across the original locus wherethe AAD-1 corn event DAS-40278-9 integrated. BLAST search also confirmedthat both 5′ end and 3′ end border sequences from the event DAS40278-9are located side by side on the same corn BAC clone.

Given the uniqueness of the 5′-integration junction of the AAD-1 cornevent DAS-40278-9, two pairs of specific PCR primers,1F5EndT1F/1F5EndT1R and Corn278-F/Corn278-R, were designed to amplifythis insert-to-plant genome junction. As predicted, the desired DNAfragment was only generated in the genomic DNA of the AAD-1 corn eventDAS-40278-9 but not any other transgenic or non-transgenic corn lines.Therefore, those two primer pairs can be used as AAD-1 corn eventDAS-40278-9 event-specific identifiers.

Example 4 Genomic Characterization Via Flanking SSR Markers ofDAS-40278-9

To characterize and describe the genomic insertion site, markersequences located in proximity to the insert were determined. A panel ofpolymorphic SSR markers were used to identify and map the transgenelocation. Event pDAS 1740-278 is located on chromosome 2 atapproximately 20 cM between SSR markers UMC1265 and MMC0111 atapproximately 20 cM on the 2008 DAS corn linkage map. Table 6Asummarizes the primer information for these two makers found to be inclose proximity to transgene pDAS1740-278.

TABLE 6APrimer names, dye labels, locus positions, forward and reverse primersequences, and significant notes for flanking makers associated withevent pDAS1740-278. Primer Name Label Chr ~cM Bin Forward PrimerReverse Primer Notes umc1265 NED 2 20 2.02 Seq ID No: 30: Seq ID No: 31:Left 5′-GCCTAGTCGCC 5′-TGTGTTCTTGATT flanking TACCCTACCAAT- GGGTGAGACAT-marker 3′ 3′ mmc0111 FAM 2 20 2.03 Seq ID No: 32: Seq ID No: 33: Right5′-TACTGGGG 5′-AATCTATGT flanking ATTAGAGCAGAAG- GTGAACAGCAGC- marker 3′3′

Example 4.1 gDNA Isolation

gDNA was extracted from leaf punches using the DNEasy 96 Plant Test Kit(Qiagen, Valencia, Calif.). Modifications were made to the protocol toaccommodate for automation. Isolated gDNA was quantified using thePicoGreen® dye from Molecular Probes, Inc. (Eugene, Oreg.). Theconcentration of gDNA was diluted to 5 ng/μl for all samples usingsterile deionized water.

Example 4.2 Screening of gDNA with Markers

The diluted gDNA was genotyped with a subset of simple sequence repeats(SSR) markers. SSR markers were synthesized by Applied Biosystems(Foster City, Calif.) with forward primers labeled with either 6-FAM,HEX/VIC, or NED (blue, green and yellow, respectively) fluorescent tags.The markers were divided into groups or panels based upon theirfluorescent tag and amplicon size to facilitate post-PCR multiplexingand analysis.

PCR was carried out in 384-well assay plates with each reactioncontaining 5 ng of genomic DNA, 1.25×PCR buffer (Qiagen, Valencia,Calif.), 0.20 μM of each forward and reverse primer, 1.25 mM MgCl₂,0.015 mM of each dNTP, and 0.3 units of HotStart Taq DNA polymerase(Qiagen, Valencia, Calif.). Amplification was performed in a GeneAmp PCRSystem 9700 with a 384-dual head module (Applied Biosystems, FosterCity, Calif.). The amplification program was as follows: (1) initialactivation of Taq at 95° C. for 12 minutes; (2) 30 sec at 94° C.; (3) 30sec at 55° C.; (4) 30 sec at 72° C.; (5) repeat steps 2-4 for 40 cycles;and (6) 30 min final extension at 72° C. The PCR products for each SSRmarker panel were multiplexed together by adding 2 μl of each PCRproduct from the same plant to sterile deionized water for a totalvolume of 60 μl. Of the multiplexed PCR products, 0.5 ul were stampedinto 384-well loading plates containing 5 μl of loading buffer comprisedof a 1:100 ratio of GeneScan 500 base pair LIZ size standard and ABIHiDi Formamide (Applied Biosystems, Foster City, Calif.). The sampleswere then loaded onto an ABI Prism 3730xl DNA Analyzer (AppliedBiosystems, Foster City, Calif.) for capillary electrophoresis using themanufacturer's recommendations with a total run time of 36 minutes.Marker data was collected by the ABI Prism 3730xl Automated SequencerData Collection software Version 4.0 and extracted via GeneMapper 4.0software (Applied Biosystems) for allele characterization and fragmentsize labeling.

Example 4.3 SSR Marker Results

The primer data for the flanking markers which were identified in theclosest proximity to the transgene are listed in Table 6. The twoclosest associated markers, UMC1265 and MMC0111, are locatedapproximately 20 cM away from the transgene insert on chromosome 2.

Example 5 Characterization of Acid-1 Protein in Event DAS-40278-9

The biochemical properties of the recombinant aad-1 protein derived fromthe transgenic maize event DAS-40278-9 were characterized. Sodiumdodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE, stainedwith Coomassie blue and glycoprotein detection methods), western blot,immunodiagnostic test strip assays, matrix assisted laserdesorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)and protein sequencing analysis by tandem MS were used to characterizethe biochemical properties of the protein.

Example 5.1 Immunodiagnostic Strip Assay

The presence of the aad-1 protein in the leaf tissue of DAS-40278-9 wasconfirmed using commercially prepared immunodiagnostic test strips fromAmerican Bionostica. The strips were able to discriminate betweentransgenic and nontransgenic plants by testing crude leaf extracts (datanot shown). The non-transgenic extracts (XHH13) did not containdetectable amounts of immunoreactive protein. This result was alsoconfirmed by western blot analysis.

To test for the expression of the aad-1 protein, an immunodiagnosticstrip analysis was performed. Four leaf punches were collected from eachplant for XHH13 (control plant) and event DAS-40278-9 bp pinching thetissue between the snap-cap lids of individually labeled 1.5-mLmicrofuge tubes. Upon receipt in the lab, 0.5 mL of aad-1 extractionbuffer (American Bionostica, Swedesboro, N.J.) was added to each tube,and the tissue was homogenized using a disposable pestle followed byshaking the sample for ˜10 seconds. After homogenization, the test stripwas placed in the tube and allowed to develop for ˜5 minutes. Thepresence or absence of the aad-1 protein in the plant extract wasconfirmed based on the appearance (or lack of appearance) of a test lineon the immunodiagnostic strip. Once the expression of the aad-1 proteinwas confirmed for the transgenic event, the maize stalk tissue washarvested and lyophilized and stored at approximately −80° C. until use.

Example 5.2 Purification of the Aad-1 Protein from Corn

Immuno-purified, maize-derived aad-1 protein (molecular weight: ˜33 kDa)or crude aqueous extracts from corn stalk tissue were prepared. All leafand stalk tissues were harvested and transported to the laboratory asfollows: The leaves were cut from the plant with scissors and placed incloth bags and stored at approximately −20° C. for future use.Separately, the stalks were cut off just above the soil line, placed incloth bags and immediately frozen at approximately −80° C. for ˜6 hours.The stalks were then placed in a lyophilizer for 5 days to remove water.Once the tissues were completely dried they were ground to a fine powderwith dry ice and stored at approximately −80° C. until needed.

The maize-derived aad-1 protein was extracted from lyophilized stalktissue in a phosphate-based buffer (see Table 7 for buffer components)by weighing out ˜30 grams of lyophilized tissue into a chilled 1000 mLglass blender and adding 500 mL of extraction buffer. The tissue wasblended on high for 60 seconds and the soluble proteins were harvestedby centrifuging the sample for 20 minutes at 30,000×g. The pellet wasre-extracted as described, and the supernatants were combined andfiltered through a 0.45μ filter. The filtered supernatants were loadedat approximately +4° C. onto an anti-aad-1 immunoaffinity column thatwas conjugated with a monoclonal antibody prepared by StrategicBiosolution Inc. (MAb 473F1 85.1; Protein A purified; Lot #:609.03C-2-4; 6.5 mg/mL (˜35.2 mg total)) (Windham, Me.); Conjugated toCNBr-activated Sepharose 4B (GE Healthcare, Piscataway, N.J.). Thenon-bound proteins were collected and the column was washed extensivelywith pre-chilled 20 mM ammonium bicarbonate buffer, pH 8.0. The boundproteins were eluted with 3.5 M NaSCN, (Sigma, St. Louis, Mo.), 50 mMTris (Sigma, St. Louis, Mo.) pH 8.0 buffer. Seven 5-mL-fractions werecollected and fraction numbers 2

7 were dialyzed overnight at approximately +4° C. against 10 mM Tris, pH8.0 buffer. The fractions were examined by SDS-PAGE and western blot andthe remaining samples were stored at approximately +4° C. until used forsubsequent analyses.

TABLE 7 The commercially available reference substances used in thisstudy are listed in the following table: Reference Substance ProductName Lot Number Assay Reference Soybean Trypsin A component of theIA110577 Glycosylation Pierce Cat #: 1856274 Inhibitor GelCodeGlycoprotein Staining Kit Horseradish A component of the JG124509Glycosylation Pierce Cat #: 1856273 Peroxidase GelCode GlycoproteinStaining Kit Bovine Serum Pre-Diluted BSA FH71884A Glycosylation, PierceCat #: 23208 Albumin Fraction V Protein Assay SDS-PAGE (BSA) StandardSet and Western Blot Prestained Molecular Novex Sharp 469212 & WesternBlot Invitrogen Cat #: LC5800, Weight Markers Prestained Protein 419493Molecular Weight Markers Markers of 260, 160, 110, 80, 60, 50, 40, 30,20, 15, 10 and 3.5 kDa Molecular Weight Invitrogen Mark12 39983 &SDS-PAGE Invitrogen Cat #: LC5677, Markers Protein Marker Mix 399895Molecular Weight Markers of 200, 116.3, 97.4, 66.3, 55.4, 36.5, 31.0,21.5, 14.4, 6.0, 3.5 and 2.5 kDa

The protein that bound to the immunoaffinity column was examined bySDSPAGE and the results showed that the eluted fractions contained theaad-1 protein at an approximate molecular weight of 33 kDa. In addition,a western blot was also performed and was positive for the aad-1protein. The maize-derived aad-1 protein was isolated from ˜30 g oflyophilized stalk material.

Example 5.3 SDS-PAGE and Western Blot

Lyophilized tissue from event DAS-40278-9 and XHH13 stalk (˜100 mg) wereweighed out in 2-mL microfuge tubes and extracted with ˜1 mL of PBST(Sigma, St. Louis, Mo.) containing 10% plant protease inhibitor cocktail(Sigma, St. Louis, Mo.). The extraction was facilitated by adding 4small ball bearings and Geno-Grinding the sample for 1 minute. Aftergrinding, the samples were centrifuged for 5 minutes at 20,000×g and thesupernatants were mixed 4:1 with 5× Laemmli sample buffer (2% SDS, 50 mMTris pH 6.8, 0.2 mg/mL bromophenol blue, 50% (w/w) glycerol containing10% freshly added 2-mercaptoethanol) and heated for 5 minutes at ˜100°C. After a brief centrifugation, 45 μL of the supernatant was loadeddirectly onto a BioRad Criterion SDS-PAGE gel (Bio-Rad, Hercules,Calif.) fitted in a Criterion Cell gel module. A positive referencestandard of microbe-derived aad-1 was resuspended at 1 mg/mL in PBST pH7.4 and further diluted with PBST. The sample was then mixed withBio-Rad Laemmli buffer with 5% 2-mercaptoethanol and processed asdescribed earlier. The electrophoresis was conducted withTris/glycine/SDS buffer (Bio-Rad, Hercules, Calif.) at voltages of150-200 V until the dye front approached the end of the gel. Afterseparation, the gel was cut in half and one half was stained with PierceGelCode Blue protein stain and the other half was electro-blotted to anitrocellulose membrane (Bio-Rad, Hercules, Calif.) with a Minitrans-blot electrophoretic transfer cell (Bio-Rad, Hercules, Calif.) for60 minutes under a constant voltage of 100 volts. The transfer buffercontained 20% methanol and Tris/glycine buffer from Bio-Rad. Forimmunodetection, the membrane was probed with an aad-1 specificpolyclonal rabbit antibody (Strategic Biosolution Inc., Newark, Del.,Protein A purified rabbit polyclonal antibody Lot #: DAS F1 197-15 1,1.6 mg/mL). A conjugate of goat anti-rabbit IgG (H+L) and alkalinephosphatase (Pierce Chemical, Rockford, Ill.) was used as the secondaryantibody. SigmaFast BCIP/NBT substrate was used for development andvisualization of the immunoreactive protein bands. The membrane waswashed extensively with water to stop the reaction and a record of theresults was captured with a digital scanner (Hewlett Packard, Palo Alto,Calif.).

In the P. fluorescens-produced aad-1 the major protein band, asvisualized on Coomassie stained SDS-PAGE gels, was approximately 33 kDa.As expected, the corresponding maize-derived aad-1 protein (eventDAS-40278-9) was identical in size to the microbe-expressed proteins.Predictably, the plant purified fractions contained a minor amount ofnon-immunoreactive impurities in addition to the aad-1 protein. Theco-purified proteins were likely retained on the column by weakinteractions with the column matrix or leaching of the monoclonalantibody off of the column under the harsh elution conditions. Otherresearchers have also reported the non-specific adsorption of peptidesand amino acids on cyanogen-bromide activated Sepharose 4Bimmunoadsorbents (Kennedy and Barnes, 1983; Holroyde et al., 1976;Podlaski and Stem, 2008).

The Pseudomonas-derived aad-1 protein showed a positive signal of theexpected size by polyclonal antibody western blot analysis. This wasalso observed in the DAS-40278-9 transgenic maize stalk extract. In theaad-1 western blot analysis, no immunoreactive proteins were observed inthe control XHH13 extract and no alternate size proteins (aggregates ordegradation products) were seen in the transgenic samples.

Example 5.4 Detection of Post-Translational Glycosylation

The immunoaffinity chromatography-purified, maize-derived aad-1 protein(Fraction #3) was mixed 4:1 with 5× Laemmli buffer. The microbe-derivedaad-1, soybean trypsin inhibitor, bovine serum albumin and horseradishperoxidase were diluted with Milli-Q water to the approximateconcentration of the plant-derived aad-1 and mixed with Bio-Rad Laemmlibuffer. The proteins were then heated at ˜95° C. for 5 minutes andcentrifuged at 20000×g for 2 minutes to obtain a clarified supernatant.The resulting supernatants were applied directly to a Bio-RadCriterionGel and electrophoresed with XT MES running buffer (Bio-Rad, Hercules,Calif.) essentially as described above except that the electrophoresiswas run at 170 V for ˜60 minutes. After electrophoresis, the gel was cutin half and one half was stained with GelCode Blue stain for totalprotein according to the manufacturers' protocol. After the staining wascomplete, the gel was scanned with a Molecular Dynamics densitometer toobtain a permanent visual record of the gel. The other half of the gelwas stained with a GelCode Glycoprotein Staining Kit (Pierce Chemical,Rockford, Ill.) according to the manufacturers' protocol to visualizeglycoproteins. The glycoproteins (with a detection limit as low as 0.625ng per band) were visualized as magenta bands on a light pinkbackground. After the glycoprotein staining was complete, the gel wasscanned with a Hewlett Packard digital scanner to obtain a permanentvisual record of the gel. After the image of the glycosylation stainingwas captured, the gel was stained with GelCode Blue to verify thepresence of the non-glycosylated proteins. The results showed that boththe maize- and microbe-derived aad-1 proteins had no detectablecovalently linked carbohydrates. This result was also confirmed bypeptide mass fingerprinting.

Example 5.5 Mass Spectrometry Peptide Mass Fingerprinting and Sequencingof Maize- and Pseudomonas-Derived Aad-1

Mass Spectrometry analysis of the Pseudomonas- and maize-derived aad-1was conducted. The aad-1 protein derived from transgenic corn stalk(event DAS-40278-9) was subjected to in-solution digestion by trypsinfollowed by MALDI-TOF MS and ESI-LC/MS. The masses of the detectedpeptides were compared to those deduced based on potential proteasecleavage sites in the sequence of maize-derived aad-1 protein. Thetheoretical cleavage was generated in silico using Protein AnalysisWorksheet (PAWS) freeware from Proteometrics LLC. The aad-1 protein,once denatured, is readily digested by proteases and will generatenumerous peptide peaks.

In the trypsin digest of the transgenic-maize-derived aad-1 protein(event DAS-40278-9), the detected peptide fragments covered nearly theentire protein sequence lacking only one small tryptic fragment at theC-terminal end of the protein, F²⁴⁸ to R²⁵³ and one short (2 aminoacids) peptide fragment. This analysis confirmed the maize-derivedprotein amino acid sequence matched that of the microbe-derived aad-1protein. Results of these analyses indicate that the amino acid sequenceof the maize-derived aad-1 protein was equivalent to the P.fluorescens-expressed protein.

Example 5.5.1 Tryptic Peptide Fragment Sequencing

In addition to the peptide mass fingerprinting, the amino acid residuesat the N- and C-termini of the maize-derived aad-1 protein(immunoaffinity purified from maize event DAS-40278-9) were sequencedand compared to the sequence of the microbe-derived protein. The proteinsequences were obtained, by tandem mass spectrometry, for the first 11residues of the microbe- and maize-derived proteins (Table 8). The aminoacid sequences for both proteins were A′ H A A L S P L S Q R″ (SEQ IDNO:30) showing the N-terminal methionine had been removed by anaminopeptidase (Table 8). The N-terminal aad-1 protein sequence wasexpected to be M′ A H A A L S P L S Q R′². (SEQ ID NO:31) These resultssuggest that during or after translation in maize and P. fluorescens,the N-terminal methionine is cleaved by a methionine aminopeptidase(MAP). MAPs cleave methionyl residues rapidly when the second residue onthe protein is small, such as Gly, Ala, Ser, Cys, Thr, Pro, and Val(Walsh, 2006). In addition to the methionine being removed, a smallportion of the N-terminal peptide of the aad-1 protein was shown to havebeen acetylated after the N-terminal methionine was cleaved (Table 8).This result is encountered frequently with eukaryotic (plant) expressedproteins since approximately 80-90% of the N-terminal residues aremodified (Polevoda and Sherman, 2003). Also, it has been shown thatproteins with serine and alanine at the N-termini are the mostfrequently acetylated (Polevoda and Sherman, 2002). The twocotranslational processes, cleavage of N-terminal methionine residue andN-terminal acetylation, are by far the most common modifications andoccur on the vast majority (˜85%) of eukaryotic proteins (Polevoda andSherman, 2002). However, examples demonstrating biological significanceassociated with N-terminal acetylation are rare (Polevoda and Sherman,2000).

TABLE 8Summary of N-terminal Sequence Data of AAD-1 Maize- and Microbe-DerivedProteins Source Expected N-terminal Sequence¹ P. fluorescensM¹AHAALSPLSQR¹² (SEQ ID NO: 31) Maize Event DAS-40278-9 M¹AHAALSPLSQR¹²Relative³ Source Expected N-terminal Sequence² Abundance P. fluorescensAHAALSPLSQR¹² 100% Maize Event DAS-40278-9 AHAALSPLSQR¹²  31%Maize Event DAS-40278-9 ^(N-Ac)AHAALSPLSQR¹²   3% (SEQ ID NO: 30)Maize Event DAS-40278-9 HAALSPLSQR¹²  50% (SEQ ID NO: 32)Maize Event DAS-40278-9 AALSPLSQR¹²   6% (SEQ ID NO: 33)Maize Event DAS-40278-9 ALSPLSQR¹²  12% (SEQ ID NO: 34) ¹ExpectedN-terminal sequence of the first 12 amino acid residues of P.fluorescens-and maize-derived AAD-1 ²Detected N-terminal sequences of P.fluorescens-and maize-derived AAD-1. ³The tandem MS data for theN-terminal peptides revealed a mixture of AHAALSPLSQR (acetylated) andN-Acetyl-AHAALSPLSQR (acetylated). ″Ragged N-terminal ends″ were alsodetected (peptides corresponding to amino acid sequences HAALSPLSQR,AALSPLSQR, and ALSPLSQR). The relative abundance, an estimate ofrelative peptide fragment quantify, was made based on the correspondingLC peak areas measured at 214 nm. Notes: Numbers in superscript (Rx)indicate amino acid residue numbers in the sequence. Amino acid residueabbreviations: A: alanine H: histidine L: leucine M: methionine P:proline Q: glutamine R: arginine S: serine T: threonine

In addition to N-acetylation, there was also slight N-terminaltruncation that appeared during purification of the maize-derived aad-1protein (Table 8). These “ragged-ends” resulted in the loss of aminoacids A2, H³ and A⁴ (in varying forms and amounts) from themaize-derived protein. This truncation is thought to have occurredduring the purification of the aad-1 protein as the western blot probeof the crude leaf extracts contained a single crisp band at the same MWas the microbe-derived aad-1 protein. The extraction buffer for thewestern blotted samples contained an excess of a protease inhibitorcocktail which contains a mixture of protease inhibitors with broadspecificity for the inhibition of serine, cysteine, aspartic, andmetalloproteases, and aminopeptidases.

The C-terminal sequence of the maize- and microbe-derived aad-1 proteinswere determined as described above and compared to the expected aminoacid sequences (Table 9). The results indicated the measured sequenceswere identical to the expected sequences, and both the maize- andmicrobe-derived aad-1 proteins were identical and unaltered at theC-terminus.

TABLE 9 Summary of C-terminal Sequence Data of AAD-1 Maize- and MicrobeDerived Proteins Source Expected C-terminal Sequence¹ P. fluorescens²⁸⁷TTVGGVRPAR²⁹⁶ Maize Event DAS-40278-9 ²⁸⁷TTVGGVRPAR²⁹⁶(SEQ ID NO: 35) Source Detected C-terminal Sequence² P. fluorescens²⁸⁷TTVGGVRPAR²⁹⁶ Maize Event DAS-40278-9 ²⁸⁷TTVGGVRPAR²⁹⁶(SEQ ID NO: 35) ¹Expected C-terminal sequence of the last 10 amino acidresidues of P. fluorescens-and maize-derived AAD-1. ²Detected C-terminalsequences of P. fluorescens-and maize-derived AAD-1. Notes: Numbers insuperscript (Rx) indicate amino acid residue numbers in the sequence.Amino acid residue abbreviations: A: alanine G: glycine P: proline R:arginine T: threonine V: valine

Example 6 Field Expression, Nutrient Composition Analysis and AgronomicCharacteristics of a Hybrid Maize Line Containing Event DAS-40278-9

The purpose of this study was to determine the levels of AAD-1 proteinfound in corn tissues. In addition, compositional analysis was performedon corn forage and grain to investigate the equivalency between theisogenic non-transformed corn line and the transgenic corn lineDAS-40278-9 (unsprayed, sprayed with 2,4-D, sprayed with quizalofop, andsprayed with 2,4-D and quizalofop). Agronomic characteristics of theisogenic non-transformed corn line were also compared to the DAS-40278-9corn. The Field expression, composition, and agronomic trials wereconducted at six test sites located within the major corn-producingregions of the U.S and Canada. These sites represent regions of diverseagronomic practices and environmental conditions. The trials werelocated in Iowa, Illinois (2 sites), Indiana, Nebraska and Ontario,Canada.

All site mean values for the control, unsprayed AAD-1, AAD-1+quizalofop,AAD-1+2,4-D and AAD-1+both entry samples were within literature rangesfor corn. A limited number of significant differences between unsprayedAAD-1, AAD-1+quizalofop, AAD-1+2,4-D or AAD-1+both corn and the controlwere observed, but the differences were not considered to bebiologically meaningful because they were small and the results werewithin ranges found for commercial corn. Plots of the compositionresults do not indicate any biologically-meaningful treatment-relatedcompositional differences among unsprayed AAD-1, AAD-1+quizalofop,AAD-1+2,4-D or AAD-1+both corn and the control corn line. In conclusion,unsprayed AAD-1, AAD-1+quizalofop, AAD-1+2,4-D and AAD-1+both corncomposition results confirm equivalence of AAD-1 (Event DAS 40278-9)corn to conventional corn lines.

Example 6.1 Corn Lines Tested

Hybrid seed containing the DAS-40278-9 event and control plants whichare conventional hybrid seed of the same genetic background as the testsubstance line, but do not contain the DAS-40278-9 event, are listed inTable 10.

TABLE 10 Test Entry Description 1 Non-aad-1 Control 2 aad-1 unsprayed 3aad-1 sprayed w/quizalofop 4 aad-1 sprayed w/2,4-D 5 aad-1 sprayedw/2,4-D and quizalofop

The corn plants described above were grown at locations within the majorcorn growing regions of the U.S. and Canada. The six field testingfacilities, Richland, Iowa; Carlyle, Ill.; Wyoming, Ill.; Rockville,Ind.; York, Nebr.; and Branchton, Ontario, Canada (referred to as IA,IL1, IL2, IN, NE and ON) represent regions of diverse agronomicpractices and environmental conditions for corn.

The test and control corn seed was planted at a seeding rate ofapproximately 24 seeds per row with seed spacing within each row ofapproximately 10 inches (25 cm). At each site, 4 replicate plots of eachtreatment were established, with each plot consisting of 2-25 ft rows.Plots were arranged in a randomized complete block (RCB) design, with aunique randomization at each site. Each corn plot was bordered by 2 rowsof a non-transgenic maize hybrid of similar maturity. The entire trialsite was surrounded by a minimum of 12 rows (or 30 ft) of anon-transgenic maize hybrid of similar relative maturity.

Appropriate insect, weed, and disease control practices were applied toproduce an agronomically acceptable crop. The monthly maximum andminimum temperatures along with rainfall and irrigation were average forthe site. These ranges are typically encountered in corn production.

Example 6.2 Herbicide Applications

Herbicide treatments were applied with a spray volume of approximately20 gallons per acre (187 L/ha). These applications were designed toreplicate maximum label rate commercial practices. Table 11 lists theherbicides that were used.

TABLE 11 Herbicide TSN Concentration Weedar 64 026491-0006 39%, 3.76 lbae^(a)/gal, 451 g ae/l Assure II 106155 10.2%, 0.87 lb ai^(b)/gal, 104 gai/l ^(a)ae = acid equivalent. ^(b)ai = active ingredient.

2,4-D (Weedar 64) was applied as 3 broadcast over-the-top applicationsto Test Entries 4 and 5 (seasonal total of 3 lb ae/A). Individualapplications were at pre-emergence and approximately V4 and V8-V8.5stages. Individual target application rates were 1.0 lb ac/A for Weedar64, or 1120 g ae/ha. Actual application rates ranged from 1096-1231 gae/A.

Quizalofop (Assure II) was applied as a single broadcast over-the-topapplication to Test Entries 3 and 5. Application timing was atapproximately V6 growth stage. The target application rate was 0.0825 lbai/A for AssureII, or 92 g ai/ha. Actual application rates ranged from90.8-103 g ai/ha.

Example 6.3 Agronomic Data Collection and Results

Agronomic characteristics were recorded for all test entries withinBlocks 2, 3, and 4 at each location. Table 12 lists the followingcharacteristics that were measured.

TABLE 12 Trait Evaluation Timing Description of Data Early Population V1and V4 Number of plants emerged per plot. Seedling Vigor V4 Visualestimate of average vigor of emerged plants per plot Plant Vigor/InjuryApproximately 1-2 Injury from herbicide applications. weeks afterapplications Time to Silking Approximately 50% The number of accumulatedheat units from the time of Silking planting until approximately 50% ofthe plants have  

  Time to Pollen Approximately 50% The number of accumulated heat unitsfrom the time of Shed Pollen shed planting until approximately 50% ofthe plants are shedding pollen Pollen Viability Approximately 50%Evaluation of pollen color and shape over time Plant HeightApproximately R6 Height to the tip of the tassel Ear HeightApproximately R6 Height to the base of the primary ear Stalk LodgingApproximately R6 Visual estimate of percent of plants in the plot withstalks broken below the primary ear Root Lodging Approximately R6 Visualestimate of percent of plants in the plot leaning approximately 30° ormore in the first ~½ meter above the soil surface Final PopulationApproximately R6 The number of plants remaining per plot Days toMaturity Approximately R6 The number of accumulated heat units from thetime of planting until approximately 50% of the plants have reachedphysiological maturity. Stay Green Approximately R6 Overall plant healthDisease Incidence Approximately R6 Visual estimate of foliar diseaseincidence Insect Damage Approximately R6 Visual estimate of insectdamage Note: Heat Unit = ((MAX temp + MIN temp/2) −50° F.

indicates data missing or illegible when filedAn analysis of the agronomic data collected from the control, aad-1unsprayed, aad-1+2,4-D, aad-1+quizalofop, and aad-1+both entries wasconducted. For the across-site analysis, no statistically significantdifferences were observed for early population (V1 and V4), vigor, finalpopulation, crop injury, time to silking, time to pollen shed, stalklodging, root lodging, disease incidence, insect damage, days tomaturity, plant height, and pollen viability (shape and color) values inthe across location summary analysis (Table 13). For stay green and earheight, significant paired t-tests were observed between the control andthe aad-1+quizalofop entries, but were not accompanied by significantoverall treatment effects or False Discovery Rates (FDR) adjustedp-values (Table 13).

TABLE 13 Summary Analysis of Agronomic Characteristics Results AcrossLocations for the DAS-40278-9 aad-1 Corn (Sprayed and Unsprayed) andControl Sprayed Sprayed Overall Trt. Unsprayed Sprayed 2,4-D Both Effect(P-value,^(b) Quizalofop (P-value, (P-value, Analyte (Pr > F)^(a)Control Adj. P)^(c) (P-value, Adj. P) Adj. P) Early population (0.351)42.8 41.3 41.7 41.9 44.1 V1 (no. of plants) (0.303, 0.819) (0.443,8.819) (0.556, 0.819) (0.393, 0.819) Early population (0.768) 43.1 43.343.7 44.3 44.8 V4 (no. of plants) (0.883, 0984) (0.687, 0.863) (0.423,0.819) (0.263, 0.819) Seedling Vigor^(d) (0.308) 7.69 7.39 7.36 7.587.78 (0.197, 0.819) (0.161, 0.819) (0.633, 0.819) 0.729, 0.889) Finalpopulation (0.873) 40.1 39.6 39.7 39.9 41.1 (number of plants) (0.747,0.889) (0.802, 0.924) (0.943, 1.00) (0.521, 0.819) Crop Injury- NA¹ 0 00 0 0 1^(st) app.^(e) Crop Injury- (0.431) 0 0 0 0 0.28 2^(nd) app.^(e)(1.00, 1.00) (1.00, 1.00) (1.00, 1.00) (0.130, 0.819) Crop Injury- NA 00 0 0 0 3^(rd) app.^(e) Crop Injury- NA 0 0 0 0 0 4^(th) app.^(e) Timeto Silking (0.294) 1291 1291 1293 1304 1300 (heat units)^(f) (0.996,1.00) (0.781, 0.917) (0.088, 0.819) (0.224, 0.819) Time to Pollen(0.331) 1336 1331 1342 1347 1347 shed (heat units)^(f) (0.564, 0.819)(0.480, 0.819) (0.245, 0.819) (0.245, 0.819) Pollen Shape (0.872) 10.910.9 11.3 11.4 11.3 0 minutes (%)^(g) (0.931, 1.00) (0.546, 0.819)(0.439, 0.819) (0.605, 0.819) Pollen Shape (0.486) 49.2 50.8 46.4 48.151.9 30 minutes (%) (0.618, 0.819) (0.409, 0.819) (0.739, 0.889) (0.409,0.819) Pollen Shape (0.724) 74.4 74.7 73.6 73.9 75.0 60 minutes (%)(0.809, 0.924) (0.470, 0819) (0.629, 0.819) (0.629, 0.819) Pollen Shape(0.816) 82.6 82.6 82.6 82.6 82.5 120 minutes (%) (1.00, 1.00) (1.00,1.00) (1.00, 1.00) (0.337, 0.819) Pollen Color (0.524) 51.9 52.5 48.950.3 53.6 30 minutes (%) (0.850, 0.960) (0.306, 0.819) (0.573, 0.819)(0.573, 0.819) Pollen Color (0.332) 75.3 75.9 74.2 74.2 75.9 60 minutes(%) (0.612, 0.819) (0.315, 0.819) (0.315, 0.819) (0.612, 0.819) PollenColor NA 84.0 84.0 84.0 84.0 84.0 120 minutes (%) Stalk Lodging (%)(0.261) 5.11 5.22 5.00 5.00 5.00 (0.356, 0.819) (0.356, 0.819) (0.356,0.819) (0.356, 0.819) Root Lodging (%) (0.431) 0.44 0.17 0.72 0.17 0.11(0.457, 0.819) (0.457, 0.819) (0.457, 0.819) (0.373, 0.819) StayGreen^(i) (0.260) 4.67 4.28 3.92 4.17 4.11 (0.250, 0.819) (0.034^(m),0.819) (0.144, 0.819) (0.106, 0.819) Disease Incidence^(j) (0.741) 6.426.22 6.17 6.17 6.17 (0.383, 0.819) (0.265, 0.819) (0.265, 0.819) (0.265,0.819) Insect Damage^(k) (0.627) 7.67 7.78 7.78 7.72 7.56 (0.500, 0.819)(0.0500, 0.819) (0.736, 0.889) (0.500, 0.819) Days to Maturity (04.87) 2411 2413 2415 2416 2417 (heat units)^(f) (0.558, 0819) ((0.302, 0.819)(0.185, 0.819) (0.104, 0.819) Plant Height (cm) (0.676) 294 290 290 291291 (0.206, 0.819) (0.209, 0.819) (0.350, 0.819) (0.286, 0.819) EarHeight (cm) (0.089) 124 120 118 121 118 (0.089, 0.819) (0.018^(m),0.786) (0.214, 0.819) (0.016^(m), 0.786) ^(a)Overall treatment effectestimated using an F-test. ^(b)Comparison of the sprayed and unsprayedtreatments to the control using a t-test. ^(c)P-values adjusted using aFalse Discovery Rate (FDR) procedure. ^(d)Visual estimate on 1-9 scale;9 = tall plants with large robust leaves. ^(e)0-100% scale; with 0 = noinjury and 100 = dead plant. ^(f)The number of heat units that haveaccumulated from the time of planting. ^(g)0-100% scale; with % pollengrains with collapsed walls. ^(h)0-100% scale; with % pollen grains withintense yellow color. ^(i)Visual estimate on 1-9 scale with 1 no visiblegreen tissue. ^(j)Visual estimate on 1-9 scale with 1 being poor diseaseresistance. ^(k)Visual estimate on 1-9 scale with 1 being poor insectresistance. ^(l)NA = statistical analysis not performed since novariability across replicate or treatment. ^(m)Statistical differenceindicated by P-Value <0.05.

Example 6.4 Sample Collection

Samples for expression and composition analysis were collected as listedin Table 14.

TABLE 14 Approx. Samples per Entry Growth Sample Control Test EntriesBlock Tissue Stage^(a) Size Entry 1 2-5 1 Leaf V2-4 3 leaves 3 3(expression) Leaf V9 3 leaves 3 3 Pollen^(b) R1 Root^(b) R1 1 plant 3 3Leaf^(b) R1 1 plant 3 3 Forage R4 1 leaf 3 3 Whole Plant R6 2 plants^(c)3 3 Grain R6- 2 plants^(c) 1 3 3 Maturity Growth Sample Control TestEntries Block Tissue Stage^(a) Size Entry 1 2-5 2-4 Forage R4 3plants^(c) 1 1 (compo- Grain R6- 5 ears sition) Maturity ^(a)Approximategrowth stage. ^(b)The pollen, root, and leaf samples collected at R1collected from the same plant. ^(c)Two plants chopped, combined andsub-sampled for expression, or 3 plants for composition

Example 6.5 Determination of Aad-1 Protein in Corn Samples

Samples of corn were analyzed for the amount of aad-1 protein. Solubleextractable aad-1 protein is quantified using an enzyme-linkedimmunosorbent assay (ELISA) kit purchased from Beacon Analytical System,Inc. (Portland, Me.).

Samples of corn tissues were isolated from the test plants and preparedfor expression analysis by coarse grinding, lyophilizing andfine-grinding (if necessary) with a Geno/Grinder (Certiprep, Metuchen,N.J.). No additional preparation was required for pollen. The aad-1protein was extracted from corn tissues with a phosphate buffered salinesolution containing the detergent Tween-20 (PBST) containing 0.5% BovineSerum Albumin (BSA). For pollen, the protein was extracted with a 0.5%PBST/BSA buffer containing 1 mg/mL of sodium ascorbate and 2% proteaseinhibitor cocktail. The plant tissue and pollen extracts werecentrifuged; the aqueous supernatant was collected, diluted withappropriate buffer if necessary, and analyzed using an aad-1 ELISA kitin a sandwich format. The kit used the following steps. An aliquot ofthe diluted sample and a biotinylated anti-aad-1 monoclonal antibody areincubated in the wells of a microtiter plate coated with an immobilizedanti-aad-1 monoclonal antibody. These antibodies bind with aad-1 proteinin the wells and form a “sandwich” with aad-1 protein bound betweensoluble and the immobilized antibody. The unbound samples and conjugateare then removed from the plate by washing with PBST. An excess amountof streptavidin-enzyme (alkaline phosphatase) conjugate is added to thewells for incubation. At the end of the incubation period, the unboundreagents were removed from the plate by washing. Subsequent addition ofan enzyme substrate generated a colored product. Since the aad-1 wasbound in the antibody sandwich, the level of color development wasrelated to the concentration of aad-1 in the sample (i.e., lower residueconcentrations result in lower color development). The absorbance at 405nm was measured using a Molecular Devices V-max or Spectra Max 190 platereader. A calibration curve was generated and the aad-1 concentration inunknown samples was calculated from the polynomial regression equationusing Soft-MAX Pro™ software which was compatible with the plate reader.Samples were analyzed in duplicate wells with the average concentrationof the duplicate wells being reported.

A summary of the aad-1 protein concentrations (averaged across sites) inthe various corn matrices is shown in Table 15. aad-1 average proteinconcentration ranged from 2.87 ng/mg dry weight in R1 stage root to 127ng/mg in pollen. Expression results for the unsprayed and sprayed plotswere similar. The aad-1 protein was not detected in any control samples,with the exception of one control root sample from the Indiana site.

TABLE 15 Summary of Mean Concentration Levels of aad-1 Protein Measuredin the aad-1Unsprayed, aad-1 + Quizalofop, aad-1 + 2,4-D and aad-1 +Quizalofop and 2,4-D in Maize Tissues AAD-1 ng/mg Corn Tissue Dry WeightTissue Treatment Mean Std. Dev. Range V2-V4 AAD-1 Unsprayed 13.4 8.001.98-29.9 Leaf AAD-1 + Quizalofop 13.3 6.89 4.75-24.5 AAD-1 + 2,4-D 14.27.16 4.98-26.7 AAD-1_Quizalofop and 2,4-D 12.3 7.09 4.07-22.5 V9 LeafAAD-1 Unsprayed 5.96 2.50 2.67-10.9 AAD-1 + Quizalofop 5.38 1.842.52-9.15 AAD-1 + 2,4-D 6.37 2.41 3.03-10.9 AAD-1_Quizalofop and 2,4-D6.52 2.38 3.11-11.1 R1 Leaf AAD-1 Unsprayed 5.57 1.66 3.47-9.34 AAD-1 +Quizalofop 5.70 1.63 2.70-7.78 AAD-1 + 2,4-D 5.99 1.90 2.40-9.42AAD-1_Quizalofop and 2,4-D 6.06 2.27 1.55-10.2 Pollen AAD-1 Unsprayed127 36.2 56.3-210  AAD-1 + Quizalofop 108 29.9 52.2-146  AAD-1 + 2,4-D113 30.2 37.5-137  AAD-1_Quizalofop and 2,4-D 112 32.6 45.4-162  R1 RootAAD-1 Unsprayed 2.92 1.87 0.42-6.10 AAD-1 + Quizalofop 3.09 1.800.56-6.06 AAD-1 + 2,4-D 3.92 2.03 0.91-7.62 AAD-1_Quizalofop and 2,4-D2.87 1.23 1.09-5.56 R4 Forage AAD-1 Unsprayed 6.87 2.79 2.37-12.1AAD-1 + Quizalofop 7.16 2.84 3.05-11.6 AAD-1 + 2,4-D 7.32 2.46 2.36-10.6AAD-1_Quizalofop and 2,4-D 6.84 2.31 2.25-10.3 Whole AAD-1 Unsprayed4.53 2.55 0.78-8.88 plant AAD-1 + Quizalofop 4.61 2.22 0.75-8.77 AAD-1 +2,4-D 5.16 2.53 0.83-10.2 AAD-1_Quizalofop and 2,4-D 4.55 1.77 1.30-8.21Grain AAD-1 Unsprayed 5.00 1.53 2.66-8.36 AAD-1 + Quizalofop 4.63 1.511.07-6.84 AAD-1 + 2,4-D 4.98 1.78 2.94-9.10 AAD-1_Quizalofop and 2,4-D4.61 1.62 1.81-7.49 ^(a) ND—value less than the method Limit OfDetection (LOD) ^(b) Values in parentheses are between the method LODand Limit Of quantitation (LOQ).

Example 6.6 Compositional Analysis

Samples of corn forage and grain were analyzed at for nutrient contentwith a variety of tests. The analyses performed for forage included ash,total fat, moisture, protein, carbohydrate, crude fiber, acid detergentfiber, neutral detergent fiber, calcium and phosphorus. The analysesperformed for grain included proximates (ash, total fat, moisture,protein, carbohydrate, crude fiber, acid detergent fiber), neutraldetergent fiber (NDF), minerals, amino acids, fatty acids, vitamins,secondary metabolites and anti-nutrients. The results of the nutritionalanalysis for corn forage and grain were compared with values reported inliterature (see; Watson, 1982 (4); Watson, 1984 (5); ILSI CropComposition Database, 2006 (6); OECD Consensus Document on CompositionalConsiderations for maize, 2002 (7); and Codex Alimentarius Commission2001 (8)).

Example 6.6.1 Proximate, Fiber and Mineral Analysis of Forage

An analysis of the protein, fat, ash, moisture, carbohydrate, ADF, NDF,calcium and phosphorus in corn forage samples from the control,unsprayed aad-1, aad-1+quizalofop, aad-1+2,4-D and aad-1+both entrieswas performed. A summary of the results across all locations is shown inTable 16. For the across-site and individual-site analysis, allproximate, fiber and mineral mean values were within literature ranges.No statistical differences were observed in the across-site analysisbetween the control and transgenic entries for moisture, ADF, NDF,calcium and phosphorus. For protein and ash, significant paired t-testswere observed for the unsprayed AAD-1 (protein), the aad-1+quizalofop(protein), and aad-1+both (ash), but were not accompanied by significantoverall treatment effects or FDR adjusted p-values. For fat, both asignificant paired t-test and adjusted p-value was observed foraad-1+quizalofop compared with the control, but a significant overalltreatment effect was not observed. For carbohydrates, a statisticallysignificant overall treatment effect, paired t-test and FDR adjustedp-value was observed between the aad-1+quizalofop and the control. Alsofor carbohydrates, a significant paired t-test for the unsprayed aad-1entry was observed, but without a significant FDR adjusted p-value.These differences are not biologically meaningful since all across-siteresults for these analytes were within the reported literature rangesfor corn, and differences from the control were small (<23%).

TABLE 16 Summary of the Proximate, Fiber and Mineral Analysis of CornForage from All Sites. Overall Sprayed Sprayed Sprayed TreatmentUnsprayed Quizalofop 2,4-D Both Literature Effect (P-value^(c) (P-value,(P-value, (P-value, Values^(a) (Pr > F)^(b) Control Adj. P)^(d) Adj. P)Adj. P) Adj. P) Proximate (% dry weight) Protein 3.14-15.9 (0.054) 7.656.51 6.41 7.17 7.13 (0.016^(c), 0.066) (0.010^(c), 0.051) (0.285, 0.450)(0.245, 0.402) Fat 0.296-6.7  (0.068) 2.29 2.08 1.78 2.10 2.01 (0.202,0.357) (0.005^(e), 0.028^(e)) (0.233, 0.391) (0.093, 0.213) Ash 1.3-10.5 (0.072) 3.90 3.84 4.03 3.99 4.40 (0.742, 0.859) (0.525, 0.708)(0.673, 0.799) (0.019e, 0.069) Moisture 53.3-87.5 (0.819) 69.5 69.2 69.569.8 70.0 (0.651, 0.782) (0.988, 0.988) (0.699, 0.820) (0.501, 0.687)Carbohydrates 66.9-94.5 (0.026^(e)) 86.1 87.6 87.8 86.8 86.5 (0.015^(e),0.061) (0.006^(e), 0.034^(e)) (0.262, 0.424) (0.538, 0.708) Fiber (% dryweight) Acid 16.1-47.4 (0.968) 26.5 26.6 26.8 26.0 26.8 Detergent(0.925, 0.970) (0.833, 0.925) (0.677, 0.800) (0.851, 0.937) Fiber (ADF)Neutral 20.3-63.7 (0.345) 41.6 43.6 43.3 41.3 41.6 Detergent (0.169,0.322) (0.242, 0.402) (0.809, 0.911) (0.978, 0.985) Fiber (NDF) Minerals(% dry weight) Calcium 0.071-0.6  (0.321) 0.212 0.203 0.210 0.215 0.231(0.532, 0.708) (0.930, 0.970) (0.815, 0.911) (0.150, 0.296) Phosphorus0.094-0.55  (0.163) 0.197 0.189 0.202 0.203 0.200 (0.198, 0.354) (0.427,0.615) (0.288, 0.450) (0.608, 0.762) ^(a)Combined range. ^(b)Overalltreatment effect estimated using an F-test. ^(c)Comparison of thetransgenic treatments to the control using t-tests. ^(d)P-valuesadjusted using a False Discovery Rate (FDR) procedure. ^(e)Statisticaldifference indicated by P-value <0.05.

Example 6.6.2 Proximate and Fiber Analysis of Grain

A summary of the results for proximates (protein, fat, ash, moisture,cholesterol and carbohydrates) and fiber (ADF, NDF and total dietaryfiber) in corn grain across all locations is shown in Table 17. Allresults for proximates and fiber were within literature ranges, and nosignificant differences in the across-site analysis were observedbetween the control and transgenic entries for fat, ash, NDF and totaldietary fiber. For moisture, a significant overall treatment effect wasobserved, but not accompanied by significant paired t-tests or FDRadjusted p-values. For ADF, a significant paired t-test was observed foraad-1+both, but no significant overall treatment effect or FDR adjustedp-value was seen. For both protein and carbohydrates, significantpair-tests, adjusted p-values and overall treatment effects were foundfor the unsprayed aad-1, aad-1+quizalofop, and aad-1+both. Since thesedifferences were small (<12%) and all values were within literatureranges, the differences are not considered biologically meaningful.

TABLE 17 Summary of the Proximate and Fiber Analysis of Corn Grain fromAll Sites. Overall Sprayed Sprayed Sprayed Treatment UnsprayedQuizalofop 2,4-D Both Literature Effect (P-value^(c) (P-value, (P-value,(P-value, Values^(a) (Pr > F)^(b) Control Adj. P)^(d) Adj. P) Adj. P)Adj. P) Proximate (% dry weight) Protein   6-17.3 (0.003^(e)) 9.97 10.911.1 10.5 10.9 (0.002^(e), 0.016^(e)) (0.0004^(e), 0.013^(e)) (0.061,0.161) (0.002^(e), 0.015^(e)) Fat  1.2-18.8 (0.369) 4.26 4.19 4.16 4.264.22 (0.238, 0.397) (0.095, 0.215) (0.955, 0.977) (0.427, 0.615) Ash0.62-6.28 (0.553) 1.45 1.55 1.52 1.45 1.51 (0.178, 0.330) (0.364, 0.557)(0.982, 0.985) (0.397, 0.587) Moisture  6.1-40.5 (0.038^(e)) 25.1 25.524.4 24.5 24.5 (0.406, 0.594) (0.056, 0.152) (0.117, 0.254) (0.114,0.250) Cholesterol NR^(f) NA^(g) <LOQ <LOQ <LOQ <LOQ <LOQ Carbohydrate63.3-89.8 (0.005^(e)) 84.3 83.3 83.2 83.8 83.4 (0.002^(e), 0.015^(e)))(0.001^(e), 0.013^(e)) (0.074, 0.185) (0.003^(e), 0.019^(e)) Fiber (%dry weight) Acid 1.82-11.3 (0.247) 4.23 3.94 3.99 3.89 3.82 Detergent(0.130, 0.269) (0.197, 0.354) (0.078, 0.193) (0.035^(e), 0.106) Fiber(ADF) Neutral 5.59-22.6 (0.442) 10.6 10.3 9.89 9.90 10.3 Detergent(0.455, 0.638) (0.120, 0.254) (0.121, 0.254) (0.552, 0.708) Fiber (NDF)Total Dietary  8.3-35.3 (0.579) 13.4 12.8 12.9 13.1 12.9 Fiber (0.164,0.313) (0.195, 0.353) (0.487, 0.679) (0.215, 0.370) ^(a)Combined range.^(b)Overall treatment effect estimated using an F-test. ^(c)comparisonof the transgenic treatments to the control using t-tests. ^(d)P-valuesadjusted using a False Discovery Rate (FDR) procedure. ^(e)Statisticaldifference indicated by P-Value <0.05. ^(f)NR = not reported. ^(g)NA =statistical analysis was snot performed since a majority of the data was<LOQ.

Example 6.6.3 Mineral Analysis of Grain

An analysis of corn grain samples for the minerals calcium, chromium,copper, iodine, iron, magnesium, manganese, molybdenum, phosphorus,potassium, selenium, sodium, and zinc was performed. A summary of theresults across all locations is shown in Table 18. All results werewithin the reported literature ranges. For the across-site analysis, nosignificant differences were observed for calcium, copper, iron, andpotassium. Mean results for chromium, iodine, selenium and sodium werebelow the limit of quantitation of the method. For magnesium andphosphorus, significant paired t-tests were observed for the unsprayedaad-1 and the aad-1+quizalofop entries, but were not accompanied bysignificant overall treatment effects or FDR adjusted p-values. Formanganese and molybdenum, a significant paired t-test was observed forthe unsprayed aad-1, but a significant FDR adjusted p-value and overalltreatment effect was not found. For the aad-1+both entry, a significantpaired t-test was observed for zinc, but a significant FDR adjustedp-value or overall treatment effect was not present. Additionally, thesedifferences from the control were small (<13%), and all values werewithin literature ranges, when available.

TABLE 18 Summary of the Mineral Analysis of Corn Grain from All Sites.Overall Sprayed Sprayed Sprayed Minerals Treatment Unsprayed Quizalofop2,4-D Both (mg/100 g Literature Effect (P-value^(c) (P-value, (P-value,(P-value, dry wt.) Values^(a) (Pr > F)^(b) Control Adj. P)^(d) Adj. P)Adj. P) Adj. P) Calcium 1.27-100  (0.493) 4.05 4.21 4.12 4.04 4.06(0.146, 0.289) (0.505, 0.687) (0.944, 0977) (0898, 0.957) Chromium0.006-0.016 NA^(e) <LOQ <LOQ <LOQ <LOQ <LOQ Copper  0073-1.85  (0963)0.144 0.151 0.146 0.141 0.149 (0.655, 0.782) (0.890, 0.957) (0.817,0.911) (0.749, 0863) Iodine 7.3-81 NA <LOQ <LOQ <LOQ <LOQ <LOQ Iron0.1-10 (0.333) 2.49 2.60 2.56 2.51 2.59 (0.086, 0.206) (0.310, 0.482)(0.801, 0.911) (0.145, 0.289) Magnesium  59.4-1000  (0.072) 122 129 128126 127 (0.010^(f), 0.051) (0.017^(f), 0.066) (0.145, 0.289) (0.070,0.177) Manganese 0.07-5.4  (0.099) 0.525 0.551 0.524 0.526 0.532(0.025^(f), 0.082) (0.884, 0.957) (0.942, 0.977) (0.505, 0.687)Molybdenum NR (0.143) 261 229 236 244 234 (0.020^(f), 0.072) (0.067,0.173) (0.206, 0.362) (0.046, 0.132) Phosphorus 147-750 (0.102) 289 303300 299 298 (0.012^(f), 0.057) (0.035^(f), 0.106) (0.055, 0.150) (0.085,0.206) Potassium 181-720 (0.453) 362 368 359 364 357 (0.330, 0.510)(0.655, 0.782) (0.722, 0.839) (0.454, 0.638) Selenium 0.001-01   NA <LOQ<LOQ <LOQ <LOQ <LOQ Sodium  0-150 NA <LOQ <LOQ <LOQ <LOQ <LOQ Zinc0.65-3.72 (0.166) 2.26 2.32 2.34 2.29 2.37 (0.183, 0.336) (0.108, 0.238)(0.627, 0.768) (0.027^(f), 0.085) ^(a)Combined range. ^(b)Overalltreatment effect estimated using an F-test. ^(c)Comparison of thetransgenic treatments to the control using t-tests. ^(d)P-valuesadjusted using a False Discovery Rate (FDR) procedure ^(e)NA =statistical analyusis was not performed since a majority fo the data was<LOQ. ^(f)Statistical difference indicated by P-value <0.05.

Example 6.6.4 Amino Acid Analysis of Grain

Corn samples were analyzed for amino acid content in the control,unsprayed aad-1, aad-1+quizalofop, aad-1+2,4-D and aad-1+both corn, anda summary of the results over all locations and by individual field siteare shown in Table 19. Levels of all amino acids were within thereported literature ranges, and no significant differences in theacross-site analysis were observed for arginine, lysine, and tyrosine.Significant differences were observed for several of the amino acids inthe across-site analysis. In these instances, the amino acid content ofthe control was lower than the aad-1 transgenic lines, which may berelated to the overall lower protein content in the control graincompared with the aad-1 lines. For the unsprayed aad-1 entry,significant overall treatment effects along with significant pairedt-tests and FDR adjusted p-values were found for all amino acids exceptarginine, glycine, lysine, tryptophan and tyrosine. For theaad-1+quizalofop entry, significant overall treatment effects along withsignificant paired t-tests and FDR adjusted p-values were found for allamino acids except arginine, cysteine, glycine, lysine, tryptophan andtyrosine. For the aad-1+2,4-D entry, significant overall treatmenteffects along with significant paired t-tests (with significant FDRadjusted p-values) were found for all amino acids except arginine,aspartic acid, glycine, histidine, lysine, tyrosine and valine. For theaad-1+both entry, significant overall treatment effects along withsignificant paired t-tests and FDR adjusted p-values were found for allamino acids except arginine, glycine, lysine, serine, tryptophan andtyrosine. Although there were many differences observed for amino acids,the differences were small (<15%), not observed across all sites, andall mean values were within reported literature ranges.

TABLE 19 Summary of the Amino Acid Analysis of Corn Grain from AllSites. Overall Sprayed Sprayed Sprayed Treatment Unsprayed Quizalofop2,4-D Both Amino Acids Literature Effect (P-value^(c) (P-value,(P-value, (P-value, (% dry wt.) Values^(a) (Pr > F)^(b) Control Adj.P)^(d) Adj. P) Adj. P) Adj. P) Alanine 0.44-1.39 (0.002^(e)) 0.806 0.9010.900 0.863 0.894 (0.0005^(e), 0.013^(e)) (0.005^(e), 0.013^(e))(0.021^(e), 0.074) (0.001^(e), 0.013^(e)) Arginine 0.12-0.64 (0.371)0486 0.499 0.505 0.487 0.484 (0.286, 0.450) (0.139, 0.283) (0.929,0.970) (0.897, 0.957) Aspartic 0.34-1.21 (0.010^(e)) 0.712 0.768 0.7640.743 0.762 Acid (0.002^(e), 0.015^(e)) (0.003^(e), 0.021) (0.060,0.160) (0.004^(e), 0.027^(e)) Cysteine 0.08-0.51 (0.033^(e)) 0.213 0.2250.223 0.223 0.226 (0.009^(e), 0.050^(e)) (0.020^(e), 0.072) (0.018^(e),0.067) (0.005^(e), 0.028^(e)) Glutamic 0.97-3.54 (0.001^(e)) 1.97 2.222.21 2.12 2.20 Acid (0.0003^(e), 0.013^(e)) (0.0004, 0.013^(e))(0.017^(e), 0.067) (0.001^(e), 0.013^(e)) Glycine 0.18-0.54 (0.052)0.383 0.397 0.398 0.390 0.397 (0.018^(e), 0.067) (0.013^(e), 0.059)(0.217, 0.371) (0.016^(e), 0.066) Histidine 0.14-0.43 (0.005^(e)) 0.2830.303 0.302 0.295 0.302 (0.001^(e), 0.013^(e)) (0.002^(e), 0.014^(e))(0.036, 0.109) (0.002^(e), 0.014^(e)) Isoleucine 0.18-0.71 (0.003^(e))0.386 0.427 0.427 0.410 0.431 (0.001^(e), 0.014^(e)) (0.001^(e),0.014^(e)) (0.044^(e), 0127) (0.001^(e), 0.013^(e)) Leucine 0.64-2.49(0.001^(e)) 1.35 1.54 1.54 1.47 1.53 (0.0003^(e), 0.013^(e)) (0.003^(e),0.013^(e)) (0.013^(e), 0.059) (0.001^(e), 0.013^(e)) Lysine 0.05-056(0.211) 0.310 0.315 0.316 0.309 0.316 (0.210, 0.367) (0.128, 0.265)(0.879, 0.956) (0.102, 0.226) Methionine 0.10-0.47 (0.003^(e)) 0.1950.209 0.209 0.205 0.208 (0.001^(e), 0.013^(e)) (0.001e, 0.013^(e))(0.014^(e), 0.061) (0.001^(e), 0.014^(e)) Phenyl- 0.24-0.93 (0.002^(e))0551 0.617 0.619 0.592 0.615 alanine (0.001^(e), 0.013^(e)) (0.001^(e),0.013^(e)) (0.023^(e), 0.077) (0.001^(e), 0.013^(e)) Proline 0.46-1.63(0.002^(e)) 0.910 1.01 1.01 0.975 0.997 (0.0004^(e), 0.013^(e))(0.001^(e), 0.013^(e)) (0.012^(e), 0.059) (0.001^(e), 0.014^(e)) Serine0.24-0.91 (0.009^(e)) 0.498 0.550 0.550 0.529 0.536 (0.002^(e),0.014^(e)) (0.001^(e), 0.014^(e)) (0.042^(e), 0.122) (0.015^(e), 0.061)Threonine 0.22-0.67 (0.005^(e)) 0.364 0394 0394 0.384 0.390 (0.001^(e),0.014^(e)) (0.001e, 0.013^(e)) (0.023^(e), 0.077) (0.003^(e), 0.020^(e))Tryptophan 0.03-0.22 0.088) 0.052 0.055 0.056 0.056 0.056 (0.067, 0.173)(0.025^(e), 0.082) (0.014^(e), 0.060) (0.029^(e), 0.092) Tyrosine0.10-0.79 (0.390) 0.336 0.355 0.375 0.339 0.314 (0.535, 0.708) (0.214,0.370) (0.907, 0.964) (0.500, 0.687) Valine 0.21-0.86 (0.005^(e)) 0.4950.537 0.538 0.519 0.538 (0.002^(e), 0.014^(e)) (0.002^(e), 0.014^(e))(0.054, 0.148) (0.001^(e), 0.014^(e)) ^(a)Combined range. ^(b)Overalltreatment effect estimated using an F-test. ^(c)Comparison of thetransgenic treatments to the control using t-tests. ^(d)P-valuesadjusted using a False Discovery Rate (FDR) procedure ^(e)Statisticaldifference indicated by P-value <0.05.

Example 6.6.5 Fatty Acid Analysis of Grain

An analysis of corn grain samples for fatty acids was performed. Asummary of the results across all locations is shown in Table 20. Allresults for the control, unsprayed aad-1, aad-1+quizalofop, aad-1+2,4-Dand aad-1+both corn grain samples analyzed for these fatty acids werewithin the published literature ranges. Results for caprylic (8:0),capric (10:0), lauric (12:0), myristic (14:0), myristoleic (14:1),pentadecanoic (15:0), pentadecenoic (15:1), heptadecanoic (17:0),heptadecanoic (17:1), gamma linolenic (18:3), eicosadienoic (20:2),eicosatrienoic (20:3), and arachidonic (20:4) were below the methodLimit of Quantitation (LOQ). In the across-site analysis, no significantdifferences were observed for 16:0 palmitic, 16:1 pamitoleic, 18:0stearic, 18:2 linoleic, 18:3 linolenic, and 20:0 arachidic. For 18:1oleic and 20:1 eicosenoic, significant paired t-tests were observed forthe unsprayed aad-1 (18:1) and the aad-1+2,4-D (18:1 and 20:1) entries,but were not accompanied by significant overall treatment effects or FDRadjusted p-values. For 22:0 behenic, a significant overall treatmenteffect and significant paired t-tests for aad-1+2,4-D and aad-1+bothwere found, but significant FDR adjusted p-values were not present.

TABLE 20 Summary of the Fatty Acid Analysis of Corn Grain from AllSites. Overall Sprayed Sprayed Sprayed Fatty Acids Treatment UnsprayedQuizalofop 2,4-D Both (% total Literature Effect (P-value^(d) (P-value,(P-value, (P-value, fatty acids)^(a) Values^(b) (Pr > F)^(c) ControlAdj. P)^(e) Adj. P) Adj. P) Adj. P) 8:0 Caparylic 0.13-0.34 NA^(f) <LOQ<LOQ <LOQ <LOQ <LOQ 10:0 Capric ND NA <LOQ <LOQ <LOQ <LOQ <LOQ 12:0Lauric ND-0.687 NA <LOQ <LOQ <LOQ <LOQ <LOQ 14:0 Myristic ND-0.3  NA<LOQ <LOQ <LOQ <LOQ <LOQ 14.1 Myristoleic NR NA <LOQ <LOQ <LOQ <LOQ <LOQ15:0 Pentadecanoic NR NA <LOQ <LOQ <LOQ <LOQ <LOQ 15:1 Pentadecenoic NRNA <LOQ <LOQ <LOQ <LOQ <LOQ 16:0 Palmitic   7-20.7 (0.559) 9.83 9.889.95 9.78 9.90 (0.618, 0.763) (0.280, 0.445) (0.617, 0.763) (0.544,0.708) 16:1 Palmitoleic ND-1.0  (0.552) 0.056 0.044 0.047 0.041 0.079(0.804, 0.911) (0.551, 0.708) (0.555, 0.708) (0.392, 0.582) 17:0Heptadecanoic ND-0.11  NA <LOQ <LOQ <LOQ <LOQ <LOQ 17:1 HeptadecenoicND-0.1  NA <LOQ <LOQ <LOQ <LOQ <LOQ 18:0 Stearic ND-3.4  (0.561) 2.041.98 2.01 2.00 2.02 (0.119, 0.254) (0.437, 0.626) (0.259, 0.421) (0.598,0.756) 18:1 Oleic 17.4-46   (0.076) 31.3 30.4 30.8 30.4 30.7 (0.013^(g),0.059) (0.178, 0.329) (0.015^(g), 0.061) (0092, 0.213) 18:2 Linoleic34.0-70   (0.474) 47.5 48.3 48.4 48.0 48.5 (0.189, 0.345) (0.144, 0.289)(0.453, 0.638) (0.119, 0.254) 18:3 Gamma NR NA <LOQ <LOQ <LOQ <LOQ <LOQLinolenic 18:3 Linoleic ND-2.25  (0.479) 1.04 1.05 1.06 1.04 1.06(0.537, 0.708) (0.202, 0.357) (0.842, 0.932) (0.266, 0.428) 20:4Arachidonic 0.1-2   (0.379) 0.400 0.386 0.393 0.390 0.390 (0.061, 0.161)(0.341, 0.525) (0.153, 0.297) (0.175, 0.328) 20:1 Eicosenoic 0.17-1.92(0.107) 0.232 0.226 0.230 0.223 0.227 (0.089, 0.210) (0.497, 0.687)(.013^(g), 0.059) (0.121, 0.254) 20:2 Eicosadienoic ND-0.53  NA <LOQ<LOQ <LOQ <LOQ <LOQ 20:3 Eicosatrienoic 0.275 NA <LOQ <LOQ <LOQ <LOQ<LOQ 20:4 Arachidonic 0.465 NA <LOQ <LOQ <LOQ <LOQ <LOQ 22:0 BehemicND-0.5  (0.044^(g)) 0.136 0.088 0.076 0.086 0.108 (0.093, 0.213) (0.887,0.957) (0011^(g), 0.054) (0.023^(g). 0.077) ^(a)Results converted fromunites of % dry weight to % fatty acids. ^(b)Combined range. ^(c)Overalltreatment effect estimated using an F-test. ^(d)Comparison of thetransgenic treatments to the control using t-tests. ^(e) P-valuesadjusted using a False Discovery rate (FDR) procedure. ^(f)NA =statistical analysis was not performed since a majority of the data was<LOQ. ^(g)Statistical difference indicated by P-value <0.05.

Example 6.6.6. Vitamin Analysis of Grain

The levels of vitamin A, B1, B2, B5, B6, B12, C, D, E, niacin, and folicacid in corn grain samples from the control, unsprayed aad-1,aad-1+quizalofop, aad-1+2,4-D and aad-1+both corn entries weredetermined. A summary of the results across all locations is shown inTable 21. Vitamins B12, D and E were not quantifiable by the analyticalmethods used. All mean results reported for vitamins were similar toreported literature values, when available. Results for the vitaminswithout reported literature ranges (vitamins B5 and C) were similar tocontrol values obtained (<22% difference from control). For theacross-site analysis, no statistical differences were observed, with theexception of vitamins B 1, C and niacin. Significant paired t-tests forVitamins B1 were observed between the control and unsprayed aad-1,aad-1+quizalofop, and aad-1+both, but were not accompanied bysignificant overall treatment effects or FDR adjusted p-values. Forvitamin C, a significant overall treatment effect was observed alongwith significant paired t-tests and FDR adjusted p-values foraad-1+quizalofop and aad-1+2,4-D. Similarly for niacin, a significantoverall treatment effect was observed along with significant pairedt-tests and FDR adjusted p-values for aad-1+quizalofop and aad-1+both. Asignificant paired t-test for the aad-1+2,4-D was also found for niacinfor the aad-1+2,4-D entry, but was not accompanied by a significantoverall treatment effect or FDR adjusted p-value. Since the differenceswere not observed across sites and values were within literature ranges(when available), the differences are not considered biologicallymeaningful.

TABLE 21 Summary of Vitamin Analysis of Corn Grain from All Sites.Overall Sprayed Sprayed Sprayed Vitamins Treatment Unsprayed Quizalofop2,4-D Both (mg/kg Literature Effect (P-value^(c) (P-value, (P-value,(P-value, dry weight) Values^(b) (Pr > F)^(b) Control Adj. P)^(d) Adj.P) Adj. P) Adj. P) Beta Carotene 0.19-46.8 (0.649) 1.80 1.85 1.80 1.821.87 (Vitamin A) (0.372, 0.566) (0.967, 0.983) (0770, 0.883) (0.221,0.376) Vitam B1 1.3-40  (0.068) 3.47 3.63 3.67 3.54 3.64 (Thiamin)(00.041^(e), 0.121) (0.013^(e), 0.059) (0.375, 0.567) (0.032^(e), 0.100)Vitamin B2 0.25-5.6  (0.803) 2.15 2.05 2.08 1.99 2.07 (Riboflavin)(0.443, 0.631) (0.600, 0.756) (0.227, 0.383) (0.543, 0.708) Vitamin B5NR^(f) (0.820) 5.28 5.17 5.09 5.29 5.10 (Pantothenic acid) (0.623,0.766) (0.391, 0.582) (0.968, 0.983) (0.424, 0.615) Vitamin B6 3.68-11.3(0.431) 6.52 6.57 6.66 6.66 7.08 (Pyridoxine) (0.859, 0.938) (0.652,0.782) (0.652, 0.782) (0.088, 0.210) Vitamin B12 NR NA^(g) <LOQ <LOQ<LOQ <LOQ <LOQ Vitamin C NR (0.018^(c)) 22.4 21.2 17.5 18.0 20.4 (0.268,0.429) (0.005^(c), 0.028^(e)) (0.004^(c), 0.026^(c)) (0.068, 0.173)Vitamin D NR NA <LOQ <LOQ <LOQ <LOQ <LOQ Vitamin E (alpha 1.5-68.7(0.558) <LOQ <LOQ <LOQ <LOQ <LOQ Tocopherol) Niacin (Nicotinic 9.3-70(0.013^(e)) 26.1 24.2 22.9 23.7 22.9 acid, Vit. B3) (0.050, 0.140)(0.002^(e), 0.017 ) (0.018^(e), 0.067) (0.002^(e), 0.016^(e)) Folic Acid0.15-683 (0.881) 0.594 0.588 0.574 0.592 0.597 (0.779, 0.890) (0.403,0.592) (0.931, 0.970) (0.916, 0.970) ^(a)Combined range. ^(b)Overalltreatment effect estimated using an F-test. ^(c)comparison of thetransgenic treatments to the control using t-tests. ^(d)P-valuesadjusted using a False Discovery Rate (FDR) procedure. ^(e)Statisticaldifference indicated by P-value <0.05. ^(f)NR = not reported. ^(g)NA =statistical analysis was not performed since a majority of the data was<LOQ.

Example 6.6.7 Anti-Nutrient and Secondary Metabolite Analysis of Grain

The secondary metabolite (coumaric acid, ferulic acid, furfural andinositol) and anti-nutrient (phytic acid, raffinose, and trypsininhibitor) levels in corn grain samples from the control, unsprayedaad-1, aad-1+quizalofop, aad-1+2,4-D and aad-1+both corn entries weredetermined. A summary of the results across all locations is shown inTable 22 and 23. For the across-site analysis, all values were withinliterature ranges. No significant differences between the aad-1 entriesand the control entry results were observed in the across-site analysisfor inositol and trypsin inhibitor. Results for furfural and raffinosewere below the method's limit of quantitation. Significant pairedt-tests were observed for coumaric acid (unsprayed aad-1, aad-1+2,4-Dand aad-1+both), and ferulic acid (aad-1+quizalofop and aad-1+both).These differences were not accompanied by significant overall treatmenteffects or FDR adjusted p-values and were similar to the control (<10%difference). A significant overall treatment effect, paired t-test, andFDR adjusted p-value was found for phytic acid (unsprayed aad-1). Sinceall results were within literature ranges and similar to the control(<11% difference), these differences are not considered to bebiologically meaningful.

TABLE 22 Summary of Secondary Metabolite Analysis of Corn Grain from AllSites. Overall Sprayed Sprayed Sprayed Secondary Treatment UnsprayedQuizalofop 2,4-D Both Metabolite Literature Effect (P-value^(c)(P-value, (P-value, (P-value, (% dry weight) Values^(a) (Pr > F)^(b)Control Adj. P)^(d) Adj. P) Adj. P) Adj. P) Coumaric Acid 0.003- (0.119)0.021 0.020 0.020 0.019 0.020 0.058 (0.038

, (0.090, (0.022

, (0.029

, 0.113) 0.211) 0.074) 0.091) Ferulic Acid 0.02- (0.077) 0.208 0.1990.196 0.200 0.197 0.389 (0.051, (0.010

, (0.080, (0.019

, 0.141) 0.051) 0.196) 0.069) Furfural 0.0003- NA^(f) <LOQ <LOQ <LOQ<LOQ <LOQ 0.0006 Inositol 0.0089- (0.734) 0.218 0.224 0.218 0.213 0.2110.377 (0.548, (0.973, (0.612, (0.526, 0.708) 0.984) 0.763) 0.708)^(a)Combined range. ^(b)Overall treatment effect estimated using anF-test. ^(c)Comparison of the transgenic treatments to the control usingt-tests. ^(d)P-values adjusted using a False Discovery Rate (FDR)procedure. ^(e)Statistical difference indicated by P-value <0.05. ^(f)NA= statistical analysis was not performed since a majority of the datawas <LOQ.

indicates data missing or illegible when filed

TABLE 23 Summary of Anti-Nutrient Analysis of Corn Grain from All Sites.Overall Sprayed Sprayed Sprayed Treatment Unsprayed Quizalofop 2,4-DBoth Anti-Nutrient Literature Effect (P-value^(c) (P-value, (P-value,(P-value, (% dry weight) Values^(a) (Pr > F)^(b) Control Adj. P)^(d)Adj. P) Adj. P) Adj. P) Phytic Acid 0.11- (0.046^(e)) 0.727 0.806 0.7670.755 0.761 1.57 (0.003^(e), (0.099, (0.245, (0.158, 0.020^(e)) 0.224)0.402) 0.304) Raffinose 0.02- NA^(f) <LOQ <LOQ <LOQ <LOQ <LOQ 0.32Trypsin Inhibitor 1.09- (0.742) 5.08 5.10 4.87 5.45 5.18 (TIU/mg) 7.18(0.954, (0.631, (0.387, (0.813, 0.977) 0.770) 0.582) 0.911) ^(a)Combinedrange. ^(b)Overall treatment effect estimated using an F-test.^(c)Comparison of the transgenic treatments to the control usingt-tests. ^(d)P-values adjusted using a False Discovery Rate (FDR)procedure. ^(e)Statistical difference indicated by P-value <0.05. ^(f)NA= statistical analysis was not performed since a majority of the datawas <LOQ.

Example 7 Additional Agronomic Trials

Agronomic characteristics of corn line 40278 compared to a near-isolinecorn line were evaluated across diverse environments. Treatmentsincluded 4 genetically distinct hybrids and their appropriatenear-isoline control hybrids tested across a total of 21 locations.

The four test hybrids were medium to late maturity hybrids ranging from99 to 113 day relative maturity. Experiment A tested event DAS-40278-9in the genetic background Inbred C×BC3S1 conversion. This hybrid has arelative maturity of 109 days and was tested at 16 locations (Table 24).Experiment B tested the hybrid background Inbred E×BC3S1 conversion, a113 day relative maturity hybrid. This hybrid was tested at 14locations, using a slightly different set of locations than Experiment A(Table 24). Experiments C and D tested hybrid backgrounds BC2S1conversion×Inbred D and BC2S1 conversion×Inbred F, respectively. Both ofthese hybrids have a 99 day relative maturity and were tested at thesame 10 locations.

TABLE 24 Locations of agronomic trials Experiment Location 2A 2B 2C 2DAtlantic, IA X X Fort Dodge, IA X X X X Huxley, IA X X X X Nora Springs,IA X Wyman, IA X X Lincoln, IL X Pontiac, IL X X X X Princeton, IL X XSeymour, IL X Shannon, IL X X X Viola, IL X X Bremen, IN X X X XEvansville, IN X Fowler, IN X X X X Mt. Vernon, IN X Olivia, MN X XWayne, NE X X York, NE X X Arlington, WI X X X Patteville, WI X X XWatertown, WI X X

For each trial, a randomized complete block design was used with tworeplications per location and two row plots. Row length was 20 feet andeach row was seeded at 34 seeds per row. Standard regional agronomicpractices were used in the management of the trials.

Data were collected and analyzed for eight agronomic characteristics;plant height, ear height, stalk lodging, root lodging, final population,grain moisture, test weight, and yield. The parameters plant height andear height provide information about the appearance of the hybrids. Theagronomic characteristics of percent stalk lodging and root lodgingdetermine the harvestability of a hybrid. Final population countmeasures seed quality and seasonal growing conditions that affect yield.Percent grain moisture at harvest defines the maturity of the hybrid,and yield (bushels/acre adjusted for moisture) and test weight (weightin pounds of a bushel of corn adjusted to 15.5% moisture) describe thereproductive capability of the hybrid.

Analysis of variance was conducted across the field sites using a linearmodel. Entry and location were included in the model as fixed effects.Mixed models including location and location by entry as random effectswere explored, but location by entry explained only a small portion ofvariance and its variance component was often not significantlydifferent from zero. For stock and root lodging a logarithmictransformation was used to stabilize the variance, however means andranges are reported on the original scale. Significant differences weredeclared at the 95% confidence level. The significance of an overalltreatment effect was estimated using a t-test.

Results from these agronomic characterization trials can be found inTable 25. No statistically significant differences were found for any ofthe four 40278 hybrids compared to the isoline controls (at p<0.05) forthe parameters of ear height, stalk lodging, root lodging, grainmoisture, test weight, and yield. Final population count and plantheight were statistically different in Experiments A and B,respectively, but similar differences were not seen in comparisons withthe other 40278 hybrids tested. Some of the variation seen may be due tolow levels of genetic variability remaining from the backcrossing of theDAS-40278-9 event into the elite inbred lines. The overall range ofvalues for the measured parameters are all within the range of valuesobtained for traditional corn hybrids and would not lead to a conclusionof increased weediness. In summary, agronomic characterization dataindicate that 40278 corn is biologically equivalent to conventionalcorn.

TABLE 25 Analysis of agronomic characteristics Treat- Range P- Parameter(units) ment Mean Min Max value Experiment A Plant Height (inches) AAD-196.31 94.00 99.00 0.6174 Control 95.41 95.00 98.00 Ear Height (inches)AAD-1 41.08 30.00 48.00 0.4538 Control 44.42 40.00 47.00 Stalk Lodging(%) AAD-1 3.64 0.00 27.70 0.2020 Control 2.49 0.00 28.57 Root Lodging(%) AAD-1 1.00 0.00 7.81 0.7658 Control 0.89 0.00 28.33 Final PopulationAAD-1 31.06 27.00 36.00 0.0230 (plants/acre in 1000's) Control 32.1727.00 36.00 Grain Moisture (%) AAD-1 22.10 14.32 27.80 0.5132 Control21.84 14.52 31.00 Test Weight (lb/ AAD-1 54.94 51.10 56.80 0.4123bushel) Control 54.66 51.00 56.80 Yield (bushels/acre) AAD-1 193.50138.85 229.38 0.9712 Control 187.05 99.87 256.72 Experiment B PlantHeight (inches) AAD-1 106.92 104.00 108.00 0.0178 Control 100.79 95.00104.00 Ear Height (inches) AAD-1 51.75 49.00 50.00 0.1552 Control 45.6338.00 50.00 Stalk Lodging (%) AAD-1 1.24 0.00 15.07 0.1513 Control 0.720.00 22.22 Root Lodging (%) AAD-1 0.64 0.00 6.15 0.2498 Control 0.400.00 9.09 Final Population AAD-1 31.30 26.00 37.00 0.4001 (plants/acrein 1000's) Control 30.98 25.00 35.00 Grain Moisture (%) AAD-1 23.7114.34 28.70 0.9869 Control 23.72 13.39 31.10 Test Weight (lb/ AAD-156.96 50.90 59.50 0.2796 bushel) Control 56.67 52.00 60.10 Yield(bushels/acre) AAD-1 200.08 102.32 258.36 0.2031 Control 205.41 95.35259.03 Experiment C Plant Height (inches) AAD-1 95.92 94.00 96.00 0.1262Control 90.92 90.00 90.00 Ear Height (inches) AAD-1 47.75 41.00 50.000.4630 Control 43.75 37.00 46.00 Stalk Lodging (%) AAD-1 6.74 0.00 27.470.4964 Control 5.46 0.00 28.12 Root Lodging (%) AAD-1 0.3512 0.00 7.580.8783 Control 0.3077 0.00 33.33 Final Population AAD-1 32.78 29.0036.00 0.0543 (plants/acre in 1000's) Control 31.68 24.00 35.00 GrainMoisture (%) AAD-1 19.09 13.33 25.90 0.5706 Control 19.36 13.66 26.50Test Weight (lb/ AAD-1 54.62 42.10 58.80 0.1715 bushel) Control 55.1452.80 58.40 Yield (bushels/acre) AAD-1 192.48 135.96 243.89 0.2218Control 200.35 129.02 285.58 Experiment D Stalk Lodging (%) AAD-1 7.290.00 9.26 0.4364 Control 4.17 0.00 39.06 Final Population AAD-1 29.9327.00 34.00 0.0571 (plants/acre in 1000's) Control 31.86 29.00 35.00Grain Moisture (%) AAD-1 18.74 19.40 24.40 0.4716 Control 19.32 13.3525.70 Test Weight (lb/ AAD-1 56.59 54.80 58.30 0.0992 bushel) Control55.50 52.70 57.40 Yield (bushels/acre) AAD-1 203.55 196.51 240.17 0.7370Control 199.82 118.56 264.11

Example 8 Use of Corn Event DAS-40278-9 Insertion Site for TargetedIntegration

Consistent agronomic performance of the transgene of corn eventDAS-40278-9 over several generations under field conditions suggeststhat these identified regions around the corn event DAS-40278-9insertion site provide good genomic locations for the targetedintegration of other transgenic genes of interest. Such targetedintegration overcomes the problems with so-called “position effect,” andthe risk of creating a mutation in the genome upon integration of thetransgene into the host. Further advantages of such targeted integrationinclude, but are not limited to, reducing the large number oftransformation events that must be screened and tested before obtaininga transgenic plant that exhibits the desired level of transgeneexpression without also exhibiting abnormalities resulting from theinadvertent insertion of the transgene into an important locus in thehost genome. Moreover, such targeted integration allows for stackingtransgenes rendering the breeding of elite plant lines with both genesmore efficient.

Using the disclosed teaching, a skilled person is able to targetpolynucleic acids of interest to the same insertion site on chromosome 2as that in corn event DAS-40278-9 or to a site in close proximity to theinsertion site in corn event DAS-40278-9. One such method is disclosedin International Patent Application No. WO2008/021207, hereinincorporated by reference in its entirety.

Briefly, up to 20 Kb of the genomic sequence flanking 5′ to theinsertion site and up to 20 Kb of the genomic sequence flanking 3′ tothe insertion site (portions of which are identified with reference toSEQ ID NO:29) are used to flank the gene or genes of interest that areintended to be inserted into a genomic location on chromosome 2 viahomologous recombination. The gene or genes of interest can be placedexactly as in the corn event DAS-40278-9 insertion site or can be placedanywhere within the 20 Kb regions around the corn event DAS-40278-9insertion sites to confer consistent level of transgene expressionwithout detrimental effects on the plant. The DNA vectors containing thegene or genes of interest and flanking sequences can be delivered intoplant cells via one of the several methods known to those skilled in theart, including but not limited to Agrobacterium-mediated transformation.The insertion of the donor DNA vector into the corn event DAS-40278-9target site can be further enhanced by one of the several methods,including but not limited to the co-expression or up-regulation ofrecombination enhancing genes or down-regulation of endogenousrecombination suppression genes. Furthermore, it is known in the artthat double-stranded cleavage of specific sequences in the genome can beused to increase homologous recombination frequency, therefore insertioninto the corn event DAS-40278-9 insertion site and its flanking regionscan be enhanced by expression of natural or designed sequence-specificendonucleases for cleaving these sequences. Thus, using the teachingprovided herein, any heterologous nucleic acid can be inserted on cornchromosome 2 at a target site located between a 5′ molecular markerdiscussed in Example 4 and a 3′ molecular marker discussed in Example 4,preferably within SEQ ID NO:29, and/or regions thereof as discussedelsewhere herein.

Example 9 Excision of the Pat Gene Expression Cassette from Corn EventDAS-40278-9

The removal of a selectable marker gene expression cassette isadvantageous for targeted insertion into the genomic loci of corn eventDAS-40278-9. The removal of the pat selectable marker from corn eventDAS-40278-9 allows for the re-use of the pat selectable marker intargeted integration of polynucleic acids into chromosome 4 insubsequent generations of corn.

Using the disclosed teaching, a skilled person is able to excisepolynucleic acids of interest from corn event DAS-40278-9. One suchmethod is disclosed in Provisional U.S. Patent Application No.61/297,628, herein incorporated by reference in its entirety.

Briefly, sequence-specific endonucleases such as zinc finger nucleasesare designed which recognize, bind and cleave specific DNA sequencesthat flank a gene expression cassette. The zinc finger nucleases aredelivered into the plant cell by crossing a parent plant which containstransgenic zinc finger nuclease expression cassettes to a second parentplant which contains corn event DAS-40278-9. The resulting progeny aregrown to maturity and analyzed for the loss of the pat expressioncassette via leaf painting with a herbicide which contains glufosinate.Progeny plants which are not resistant to the herbicide are confirmedmolecularly and advanced for self-fertilization. The excision andremoval of the pat expression cassette is molecularly confirmed in theprogeny obtained from the self-fertilization. Using the teachingprovided herein, any heterologous nucleic acid can be excised from cornchromosome 2 at a target site located between a 5′ molecular marker anda 3′ molecular marker as discussed in Example 4, preferably within SEQID NO:29 or the indicated regions thereof.

Example 10—Resistance to Brittlesnap

Brittlesnap refers to breakage of corn stalks by high winds followingapplications of growth regulator herbicides, usually during periods offast growth. Mechanical “push” tests, which use a bar to physically pushthe corn to simulate damage due to high winds, were performed on hybridcorn containing event DAS-40278-9 and control plants not containingevent DAS-40278-9. The treatments were completed at four differentgeographical locations and were replicated four times (there was anexception for one trial which was only replicated three times). Theplots consisted of eight rows: four rows of each of the two hybrids,with two rows containing event DAS-40278-9 and two rows without theevent. Each row was twenty feet in length. Corn plants were grown to theV4 developmental stage, and a commercial herbicide containing 2,4-D(Weedar 64, Nufarm Inc., Burr Ridge, Ill.) was applied at rates of 1120g ac/ha, 2240 g ae/ha and 4480 g ae/ha. Seven days after application ofthe herbicide, a mechanical push test was performed. The mechanical pushtest for brittlesnap consisted of pulling a 4-foot bar down the two rowsof corn to simulate wind damage. Height of the bar and speed of travelwere set to provide a low level of stalk breakage (10% or less) withuntreated plants to ensure a test severe enough to demonstrate adifference between treatments. The directionality of the brittlesnaptreatment was applied against leaning corn.

Two of the trial locations experienced high winds and thunderstorms 2-3days after application of the 2,4-D herbicide. On two consecutive days,a thunderstorm commenced in Huxley Iowa. Wind speeds of 2 to 17 m s⁻¹with high speeds of 33 m s⁻¹ were reported at the site of the fieldplot. The wind direction was variable. On one day, a thunderstorm wasreported in Lanesboro Minn. Winds of high velocity were reported at thesite of this field plot. In addition, both storms produced rain. Thecombination of rain and wind attributed to the reported brittlesnapdamage.

Assessments of the brittlesnap damage which resulted from the mechanicalpush test (and inclement weather) were made by visually rating thepercentage of injury. Prior to the mechanical brittlesnap bar treatment,plant stand counts were made for the hybrid corn containing eventDAS-40278-9 and controls. Several days after the brittlesnap bartreatment the plot stand counts were reassessed. The percentage ofleaning and percentage of reduced stand within the plot was determined(Table 26). The data from the trials demonstrated that hybrid corncontaining event DAS-40278-9 has less propensity for brittlesnap ascompared to the null plants following an application of 2,4-D.

TABLE 26 DAS-40278-9 Corn Brittlesnap Tolerance to V4 Application of2,4-D Amine. The percentage of brittlesnap was calculated for hybridcorn plants containing event DAS- 40278-9 and compared to control plantswhich do not contain the event. 278 (SL B01- Null Null 278//4X (SLB01//278 (SLB01VX- (SLB01VX// Treatment P811XTR) 4XP811XTR) 278/BE9515XT)BE9515XT) Before Mechanical Snapping Mean³ % Leaning 7-8 Days AfterApplication¹ Weedar 64 0% 38%  0% 33% 1120 g ac/ha Weedar 64 1% 42%  0%33% 2240 g ac/ha Weedar 64 2% 55%  1% 46% 4480 g ac/ha Untreated 0%  0% 0%  0% After Mechanical Snapping Mean³ % Leaning 11-14 Days AfterApplication Weedar 64 0% 19%  1% 24% 1120 g ac/ha Weedar 64 4% 30%  7%27% 2240 g ac/ha Weedar 64 4% 26%  6% 28% 4480 g ac/ha Untreated 0%  0% 0%  0% After Mechanical Snapping Mean³ % Stand Reduction 11-14 DaysAfter Application Weedar 64 3% 38%  6% 42% 1120 g ac/ha Weedar 64 9% 35%12% 41% 2240 g ac/ha Weedar 64 9% 40% 16% 40% 4480 g ac/ha Untreated 0% 0%  0%  0% ¹Thunderstorm and high winds occurred 2-3 days afterapplication in two trials ²Treatments replicated four times in arandomized complete block design (one trial was only completed for threereplications ³Means corrected for occurrences in untreated (untreatedmeans forced to zero)

Example 11 Protein Analysis of Grain

Grain with increased total protein content was produced from hybrid corncontaining event DAS-40278-9 as compared to control plants notcontaining the event. Two consecutive multisite field trails wereconducted that included non-sprayed and herbicide-treatments with threedifferent herbicide combinations. In 7 of the 8 statistical comparisons,the DAS-40278-9 event produced grain with significantly higher totalprotein content (Table 27). This data is corroborated by analyses ofindividual amino acids.

TABLE 27 Protein content of grain from multisite field trials Non- EventDAS- Event DAS- Event DAS- Event DAS-40278- 2008 Field transgenic40278-9 40278-9 40278-9 9 quizalofop Season Near-isoline unsprayedquizalofop 2,4-D and 2,4-D Mean 9.97 10.9 11.1 10.5 10.9 % increase 09.3 11.3 5.3 9.3 over isoline Paired t-test NA 0.0002 0.0004 0.061 0.002Mean 10.9 11.6 11.7 11.7 11.5 % increase 0 6.4 7.3 7.2 5.5 over isolinePaired t-test NA 0.0048 0.001 0.0012 0.0079

Example 12 Additional Agronomic Trials

Agronomic characteristics of hybrid corn containing event DAS-40278-9compared to near-isoline corn were collected from multiple field trialsacross diverse geographic environments for a growing season. The datawere collected and analyzed for agronomic characteristics as describedin Example 7. The results for hybrid corn lines containing eventDAS-40278-9 as compared to null plants are listed in Table 28.Additionally, agronomic characteristics for the hybrid corn linescontaining event DAS-40278-9 and null plants sprayed with the herbicidesquizalofop (280 g ae/ha) at the V3 stage of development and 2,4-D (2,240g ae/ha) sprayed at the V6 stage of development are described in Table29.

TABLE 28 yield, percent moisture, and final population results forhybrid corn containing event DAS-40278-9 as compared to the near-isolinecontrol. Grain Final Population Moisture (plants/acre Name Yield (%)Reported in 1000's) Hybrid Corn Containing 218.1 21.59 31.69 DAS-40278-9Control Hybrid Corn 217.4 21.91 30.42

TABLE 29 yield, percent moisture, percentage stock lodging, percentageroot lodging and total population for hybrid corn lines containing eventDAS-40278-9 as compared to the near-isoline control. Final PopulationGrain Stock Lodge Root Lodge (plants/acre reported Trial Yield Moisture(%) (%) (%) in 1000's) Spray Trial Hybrid Corn #1 214.9 23.4 0.61 2.1930 Containing DAS- 40278-9 Control Hybrid 177.9 23.46 0.97 36.32 28.36Corn #1 LSD (0.5) 13.3 1.107 0.89 10.7 1.1 Non Spray Hybrid Corn #1219.6 22.3 0.95 1.78 30.8 Containing DAS- 40278-9 Control Hybrid 220.322.51 0.54 1.52 30.55 Corn #1 LSD (0.5) 6.9 0.358 0.98 1.65 0.7 SprayTrial Hybrid Corn #2 198.6 26.76 0.38 2.08 29.29 Containing DAS- 40278-9Control Hybrid 172.3 23.76 1.5 39.16 28.86 Corn #2 LSD (0.5) 13.3 1.1070.89 10.7 1.1 Non Spray Hybrid Corn #2 207.8 24.34 0.22 0.59 31Containing DAS- 40278-9 Control Hybrid 206.2 24.88 0.35 0.12 30.94 Corn#2 LSD (0.5) 8.0 0.645 0.55 1.79 0.9

The invention claimed is:
 1. A transgenic corn plant comprising arecombinant polynucleotide that encodes an aryloxyalkanoate dioxygenase(AAD-1) protein that exhibits aryloxyalkanoate dioxygenase activity,wherein said activity enzymatically degrades a phenoxy auxin herbicideand an (R)-aryloxyphenoxypropionate herbicide, wherein said recombinantpolynucleotide hybridizes under stringent conditions with a sequenceconsisting of nucleotides 6679 to 6700 of SEQ ID NO: 29 or nucleotides1863 to 1875 of SEQ ID NO: 29, or the full complement of nucleotides6679 to 6700 of SEQ ID NO: 29 or nucleotides 1863 to 1875 of SEQ ID NO:29.
 2. The transgenic corn plant of claim 1 wherein said AAD-1 proteinhas at least 95% sequence identity with SEQ ID NO:
 9. 3. The transgeniccorn plant of claim 1 wherein said plant comprises event DAS-40278-9 aspresent in the seed deposited with American Type Culture Collection(ATCC) under Accession No. PTA-10244.
 4. A corn seed comprising arecombinant polynucleotide that encodes an aryloxyalkanoate dioxygenase(AAD-1) protein that exhibits aryloxyalkanoate dioxygenase activity,wherein said activity enzymatically degrades a phenoxy auxin herbicideand an (R)-aryloxyphenoxypropionate herbicide, wherein said recombinantpolynucleotide hybridizes under stringent conditions with a sequenceconsisting of nucleotides 6679 to 6700 of SEQ ID NO: 29 or nucleotides1863 to 1875 of SEQ ID NO: 29, or the full complement of nucleotides6679 to 6700 of SEQ ID NO: 29 or nucleotides 1863 to 1875 of SEQ ID NO:29.
 5. A corn plant produced by growing the seed of claim 4, said plantcomprising said recombinant polynucleotide.
 6. A progeny plant of thecorn plant of claim 5, said progeny plant comprising said recombinantpolynucleotide.
 7. A part of the plant of claim 5 wherein said part isselected from the group consisting of pollen, ovule, flowers, shoots,roots, and leaves, said part comprising said recombinant polynucleotide.8. A method of breeding a corn plant, said method comprising crossing afirst corn plant, comprising a recombinant polynucleotide thathybridizes under stringent conditions with a sequence consisting ofnucleotides 6679 to 6700 of SEQ ID NO: 29 or nucleotides 1863 to 1875 ofSEQ ID NO: 29, or the full complement of nucleotides 6679 to 6700 of SEQID NO: 29 or nucleotides 1863 to 1875 of SEQ ID NO: 29, with a secondcorn plant to produce a third corn plant, and assaying said third cornplant for the presence of said recombinant polynucleotide in the genomeof the third plant.
 9. A method of controlling weeds, said methodcomprising applying an aryloxyalkanoate herbicide to plants growing in afield, wherein said plants growing in the field comprise a plant ofclaim
 1. 10. The method of claim 9, wherein said herbicide is selectedfrom the group consisting of 2,4-D; 2,4-DB; 2,4-DP, MCPP, MCPA; andMCPB.
 11. The method of claim 9, wherein said herbicide is an(R)-aryloxyphenoxypropionate herbicide, optionally wherein the herbicideis (R)-quizalofop or (R)-haloxyfop.
 12. The method of claim 9, whereinsaid method comprises applying a second herbicide to said plants growingin the field.
 13. The method of claim 12, wherein said second herbicideis selected from the group consisting of glyphosate and dicamba.
 14. Amethod of controlling weeds, said method comprising applying anaryloxyalkanoate herbicide to a field, and planting the seed of claim 4in said field within 14 days after applying the herbicide.
 15. A methodof controlling glyphosate-resistant weeds in an area comprising a plantof claim 1, wherein said plant further comprises a glyphosate tolerancetrait, said method comprising applying an aryloxyalkanoate herbicide tosaid area.
 16. The method of claim 15 wherein said herbicide is aphenoxy auxin or (R)-aryloxyphenoxypropionate herbicide.
 17. The methodof claim 16 wherein said herbicide is applied from a tank mix withglyphosate.
 18. The method of claim 17 wherein at least one of saidweeds is a glyphosate-resistant volunteer of a different species thansaid plant.
 19. A method of controlling weeds in an area undercultivation, said area comprising a plurality of plants of claim 1, saidmethod comprising applying an aryloxy alkanoate herbicide over the topof the plants.
 20. A method of controlling weeds in an area undercultivation, said method comprising applying an aryloxy alkanoateherbicide to a field planted with the seed of claim 4, wherein theherbicide is applied pre-emergence, post-emergence, or pre-emergence andpost-emergence to the plants, parts of the plants, and/or to the areaunder cultivation.
 21. The method of claim 19, said method comprisingapplying said herbicide jointly with or separately from a secondherbicide.
 22. The method of claim 20, said method comprising applyingsaid herbicide jointly with or separately from a second herbicide.